External Email - Use Caution        

Hi,

I apologize if I did not explain my issue properly.
I'm interested in looking at age-related thickness reductions in 1 group (patients), but I'd like to also account for the effect of disease duration.
We can say that in my case disease duration is the nuisance factor.
Briefly, I have the same issue reported in here (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32860.html), but with only one group.
How would you recommend to proceed?

Many  thanks,

Pilar 

Message: 2
Date: Wed, 27 Nov 2019 16:56:20 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue
        36
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <fbb77a97-61b5-fac5-e2b3-0ee327e29ce3@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

what is the difference between and independent variable and a covariate?

On 11/27/2019 6:57 AM, Ferraro, Pilar wrote:
>          External Email - Use Caution
>
> Yes, I did.
> But in this case I have two factors, not only one. In particular, I have an independent variable X and a covariate I?d like to include in the model.
> How would you suggest to proceed?
>
>
> Thanks,
>
> Pilar
>
>> Message: 5
>> Date: Tue, 26 Nov 2019 21:22:34 +0000
>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Regression analysis correcting for 1
>>       variable
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <9ac0cfa1-6e63-7d67-695e-ee607f889655@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> did you look at the one group, one variable example here?
>> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V
>>
>>
>> On 11/25/2019 6:42 AM, Ferraro, Pilar wrote:
>>>          External Email - Use Caution
>>>
>>> Hi Freesurfer experts,
>>>
>>> I?ve received your last response concerning the cortical thickness comparison between patients and HC correcting for disease duration and I?ve successfully completed the procedure.
>>> Thanks again!
>>> Now I?m contacting you cause I?m running a different analysis and I?m struggling to understand how to proceed.
>>> In particular I would like to complete a regression analysis (only in patients, therefore only one group) looking at the effect of Variable X on cortical thickness (which I assume being higher X values corresponding to lower CT values), correcting for the effect of Variable Y (disease duration).
>>> When I?ve looked at the Freesurfer Wiki for finding good examples I?ve thought I can use the one group, two covariates example.
>>> However, in this case I?m not sure how the FSGD file and the matrix should be organized.
>>> I suppose the FSGD file can simply list the Input subjects, Variable X and Variable Y.
>>> Then the matrix should be 0 -1 0.
>>> Am I correct?
>>>
>>> Thanks for any help!
>>>
>>> Pilar Ferraro
>>>
>>>
>>>
>>>> ------------------------------
>>>>
>>>> Message: 3
>>>> Date: Wed, 20 Nov 2019 22:40:29 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] Fwd: surface group analysis with qdec
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <70fa9541-d854-4530-9180-d001cf008f04@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> I responded to this a few days ago. Below is what I said
>>>>
>>>> The problem is that all of your class=0 subjects have a 0 duration
>>>> meaning that you cannot compute a duration slope for this class. In this
>>>> special case, you can run a different-offset, same-slope analysis with
>>>> --fsgd dur.fsgd doss
>>>> Change your contrast matrix to 1 -1 0
>>>>
>>>>
>>>> On 11/19/19 5:00 AM, Ferraro, Pilar wrote:
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> Hi,
>>>>>
>>>>> I?ve never got a response to my last email (you can find it below).
>>>>>
>>>>> Would you be able to let me know so I can proceed with the analyses?
>>>>>
>>>>> Many thanks,
>>>>>
>>>>> Pilar
>>>>>
>>>>>> Inizio messaggio inoltrato:
>>>>>>
>>>>>> *Da: *"Ferraro, Pilar" <FerraroP@pennmedicine.upenn.edu
>>>>>> <mailto:FerraroP@pennmedicine.upenn.edu>>
>>>>>> *Oggetto: **Fw: surface group analysis with qdec*
>>>>>> *Data: *14 novembre 2019 3:47:42 PM CET
>>>>>> *A: *"freesurfer@nmr.mgh.harvard.edu
>>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>"
>>>>>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I'm trying to run a surface based group analysis comparing patients
>>>>>> and HC, correcting for disease duration.
>>>>>> I enclose here the fsgd file and the design matrix.
>>>>>> I've followed all the steps of the tutorial
>>>>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0)?with
>>>>>> no errors.
>>>>>> However, when I try to run the glm analysis with the following command:
>>>>>>
>>>>>> mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C
>>>>>> lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir
>>>>>> lh.dur.glmdir
>>>>>>
>>>>>> I get the error:
>>>>>>
>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>>>>>> --------------------------------
>>>>>> Possible problem with experimental design:
>>>>>> Check for duplicate entries and/or lack of range of
>>>>>> continuous variables within a class.
>>>>>>
>>>>>> Of course there is no range for the continuous variable (disease
>>>>>> duration) in the control group, so I'm wondering how to overcome
>>>>>> this?limit and proceed correctly with the glm analysis.
>>>>>>
>>>>>> Many thanks in advance for any help you will provide,
>>>>>>
>>>>>> Pilar
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------
>>>>>> *From:*Ferraro, Pilar
>>>>>> *Sent:*Monday, November 11, 2019 7:07 AM
>>>>>> *To:*freesurfer@nmr.mgh.harvard.edu
>>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>>>> *Subject:*surface group analysis with qdec
>>>>>> Hi!
>>>>>>
>>>>>> I've previously run a comparison between patients and HC using qdec,
>>>>>> but now I'd like to correct the analysis for disease duration.
>>>>>> I've therefore generated a second qdec.table.dat file inserting the
>>>>>> disease duration column with the following structure:
>>>>>> fsid group duration
>>>>>> Input subj1 1 13
>>>>>> Input subj2 0
>>>>>>
>>>>>> (For healthy controls group (group 0) I've tried both options,
>>>>>> leaving the duration column blank or inserting 0 as a value).
>>>>>> I've also left the group.level file the same of the previous analysis.
>>>>>> However, when i open the new qdec.table.dat file with qdec I get
>>>>>> problems in correctly uploading the data.
>>>>>> In particular, I get the following error:
>>>>>>
>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>>>>>> Possible problem with experimental design:
>>>>>> Check for duplicate entries and/or lack of range of continuous
>>>>>> variables within a class.
>>>>>> If you seek help with this problem, make sure to send:
>>>>>> ?This is the command line:
>>>>>> ?mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh
>>>>>> --fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods
>>>>>> --glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage
>>>>>> lh --label
>>>>>> /home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C
>>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
>>>>>> --C
>>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat
>>>>>>
>>>>>> Of course there is no range for the continuous variable (disease
>>>>>> duration) in the control group, so I'm wondering how to overcome this
>>>>>> and generate a?correct qdec.table.dat file.
>>>>>>
>>>>>> Thanks in advance for any help!
>>>>>>
>>>>>> Pilar
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 4
>>>> Date: Wed, 20 Nov 2019 22:45:18 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] Question about the input for longitudinal
>>>>     processing pipeline
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <8be29ed9-8627-d005-fd9b-ca3ec56f8a5b@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> I have not run images with contrast, but I think it should? work. Some
>>>> people have tried to use the mp2rage UNI scan, but it often fails
>>>> because of very bright voxels outside of the brain. If you can remove
>>>> those (eg, skull stripping), then it might work. Alternatively, if you
>>>> have a quantitative T1 that comes out of the mp2rage if you have the
>>>> license, then you can simulate an mp1rage that will then work in FS (but
>>>> it will have bias fields). If you don't have a qT1, it is not too hard
>>>> to convert the UNI to qT1. Is this at 3T or 7t?
>>>>
>>>> On 11/19/19 5:35 AM, Darko Komneni? wrote:
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> Hi Douglas,
>>>>> thanks for your reply. Indeed, in this particular data set they don't
>>>>> all have contrast, which is unfortunate. But my question was also
>>>>> general, if we assume that they all have contrast, would it be OK to
>>>>> use those images as inputs in the longitudinal pipeline? And the same
>>>>> question for mp2rage images, are they OK to use as well, or are they
>>>>> not suitable for this pipeline?
>>>>> Best,
>>>>> Darko
>>>>>
>>>>>
>>>>>     ------------------------------
>>>>>
>>>>>     Message: 11
>>>>>     Date: Mon, 18 Nov 2019 18:41:37 +0000
>>>>>     From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu
>>>>>     <mailto:DGREVE@mgh.harvard.edu>>
>>>>>     Subject: Re: [Freesurfer] Question about the input for longitudinal
>>>>>     ? ? ? ? processing pipeline
>>>>>     To: "freesurfer@nmr.mgh.harvard.edu
>>>>>     <mailto:freesurfer@nmr.mgh.harvard.edu>"
>>>>>     <freesurfer@nmr.mgh.harvard.edu
>>>>>     <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>>>     Message-ID: <d5205fe6-329a-f9b4-252a-8f1857aa42e4@mgh.harvard.edu
>>>>>     <mailto:d5205fe6-329a-f9b4-252a-8f1857aa42e4@mgh.harvard.edu>>
>>>>>     Content-Type: text/plain; charset="utf-8"
>>>>>
>>>>>     Do all images and time points have contrast? If some do and some
>>>>>     don't,
>>>>>     then I don't think you can properly do the analysis?
>>>>>
>>>>>     On 11/15/19 10:06 AM, Darko Komneni? wrote:
>>>>>> ????????External Email - Use Caution
>>>>>>
>>>>>> Dear Freesurfer experts,
>>>>>> I wanted to run the Freesurfer's longitudinal processing pipeline
>>>>>> (described here
>>>>>>
>>>>>     https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing)
>>>>>     on a
>>>>>> series of MRI scans from a single patient. However, after
>>>>>     looking at
>>>>>> the scans, i realized that for most time points, the patient
>>>>>     doesn't
>>>>>> have a "simple/normal" T1 MPRAGE sequence available. Instead, they
>>>>>> have a T1 sequence with a contrast agent, as well as T1 mp2rage
>>>>>> sequences.
>>>>>>
>>>>>> Is it possible/advisable to run recon-all in general or this
>>>>>     pipeline
>>>>>> in particular on T1 MPRAGE scans that have a contrast agent, or
>>>>>     that
>>>>>> are mp2rage instead of MPRAGE?
>>>>>>
>>>>>> Thanks in advance!
>>>>>> Best,
>>>>>> Darko
>>>>>>
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 5
>>>> Date: Wed, 20 Nov 2019 22:46:22 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] Local Gyrification Index: freesurfer version
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <2601bc80-e87a-74b3-9227-24ca60dafd97@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> It has not changed (and is no longer supported)
>>>>
>>>> On 11/19/19 6:48 AM, Steve Petersen wrote:
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> Dear Freesurfer experts,
>>>>>
>>>>> What freesurfer version do you recommend to perform the local
>>>>> gyrification index, version 6 or 6 development version?
>>>>>
>>>>>
>>>>> Thanks in advance.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 6
>>>> Date: Wed, 20 Nov 2019 22:51:21 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] Recon-all Error
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <13cb3ba0-0342-6f84-2029-2d4ac0eb914e@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> This is something that is being triggered by use -3T. Is there a reason
>>>> you are using that option?
>>>>
>>>> On 11/19/19 5:15 PM, Meena M. Makary wrote:
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> Hi,
>>>>>
>>>>> I have been getting this error with one of my subjects Recon-all. I am
>>>>> attaching the recon-all log file. any help would be appreciated!
>>>>>
>>>>> Meena
>>>>>
>>>>> --
>>>>> ?
>>>>> *Meena M. Makary, Ph.D.*
>>>>> Assistant Professor|Cairo University <http://bmes.cufe.edu.eg/>
>>>>> Postdoctoral Fellow|Radiology, Harvard?Medical School
>>>>> <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550>
>>>>> Postdoctoral Fellow| Athinoula A. Martinos Center, MGH
>>>>> <https://www.nmr.mgh.harvard.edu/user/4550386>
>>>>> Career Development and Mentoring Manager | OHBM Student and Postdoc
>>>>> SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449>
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 7
>>>> Date: Wed, 20 Nov 2019 22:54:30 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] mask for cortical thickness
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <f95d9228-9445-09c0-90d9-48f16e5a41f1@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> Pass the mask you want to mri_glmfit with either --label or --mask
>>>> (depending on your format). You can convert the aparc to labels using
>>>> mri_annotation2label , then pick the label you want. In this case, you
>>>> cannot use --cache as that has been computed using whole hemi. You can
>>>> generate your own MC simulation, but the better way to do this is with
>>>> permutation. see
>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>>>>
>>>> On 11/20/19 4:47 PM, Gwang-Won Kim wrote:
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> Hi there,
>>>>> I would like to analyze clusterwise correction for multiple
>>>>> comparisons using masks (exsample; superior frontal cortex and?middle
>>>>> frontal cortex).
>>>>> I know that "2spaces" means adjust p-values for two hemispheres as
>>>>> follow; mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 2 abs
>>>>> --2spaces.
>>>>> If I use the masks such as the superior frontal cortex and?middle
>>>>> frontal cortex,?how do I do?
>>>>> Thanks,
>>>>> Gwang-Won
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 8
>>>> Date: Wed, 20 Nov 2019 22:58:17 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue
>>>>     26
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <453c8556-e0de-cf0e-f84b-65c5273e186e@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> Sorry, I don't have your fsgd file anymore. It will be computing
>>>> FirstClass-SecondClass, so red means FirstClass>SecondClass
>>>>
>>>> On 11/19/19 6:05 AM, Ferraro, Pilar wrote:
>>>>>          External Email - Use Caution
>>>>>
>>>>> Thank you very much for your helpful reply!
>>>>> I?ve kept the same fsgd file, and just edited the contrast matrix to 1 -1 0 and added the doss option to the command line, as you suggested.
>>>>> I?m just a little bit confused cause now I get by default blue and red regions when I visualize the results in Freeview. Am I correct assuming that blue regions are the ones where cortical thickness is reduced in patients relative to HC correcting for disease duration?
>>>>> I just wanted to ask for a confirmation since in my fsgd file class 1 (patients) comes first and then class 0 (hc).
>>>>>
>>>>> Many thanks,
>>>>>
>>>>> Pilar
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 6
>>>>>> Date: Mon, 18 Nov 2019 18:28:58 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] Fw: surface group analysis with qdec
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <b967bd8b-5fb9-0c00-7207-3944fad5c09a@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="Windows-1252"
>>>>>>
>>>>>> The problem is that all of your class=0 subjects have a 0 duration
>>>>>> meaning that you cannot compute a duration slope for this class. In this
>>>>>> special case, you can run a different-offset, same-slope analysis with
>>>>>> --fsgd dur.fsgd doss
>>>>>> Change your contrast matrix to 1 -1 0
>>>>>>
>>>>>>
>>>>>> On 11/14/19 9:47 AM, Ferraro, Pilar wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I'm trying to run a surface based group analysis comparing patients
>>>>>>> and HC, correcting for disease duration.
>>>>>>> I enclose here the fsgd file and the design matrix.
>>>>>>> I've followed all the steps of the tutorial
>>>>>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0)?with
>>>>>>> no errors.
>>>>>>> However, when I try to run the glm analysis with the following command:
>>>>>>>
>>>>>>> mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C
>>>>>>> lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir
>>>>>>> lh.dur.glmdir
>>>>>>>
>>>>>>> I get the error:
>>>>>>>
>>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>>>>>>> --------------------------------
>>>>>>> Possible problem with experimental design:
>>>>>>> Check for duplicate entries and/or lack of range of
>>>>>>> continuous variables within a class.
>>>>>>>
>>>>>>> Of course there is no range for the continuous variable (disease
>>>>>>> duration) in the control group, so I'm wondering how to overcome
>>>>>>> this?limit and proceed correctly with the glm analysis.
>>>>>>>
>>>>>>> Many thanks in advance for any help you will provide,
>>>>>>>
>>>>>>> Pilar
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>> *From:* Ferraro, Pilar
>>>>>>> *Sent:* Monday, November 11, 2019 7:07 AM
>>>>>>> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
>>>>>>> *Subject:* surface group analysis with qdec
>>>>>>> Hi!
>>>>>>>
>>>>>>> I've previously run a comparison between patients and HC using qdec,
>>>>>>> but now I'd like to correct the analysis for disease duration.
>>>>>>> I've therefore generated a second qdec.table.dat file inserting the
>>>>>>> disease duration column with the following structure:
>>>>>>> fsid group duration
>>>>>>> Input subj1 1 13
>>>>>>> Input subj2 0
>>>>>>>
>>>>>>> (For healthy controls group (group 0) I've tried both options, leaving
>>>>>>> the duration column blank or inserting 0 as a value).
>>>>>>> I've also left the group.level file the same of the previous analysis.
>>>>>>> However, when i open the new qdec.table.dat file with qdec I get
>>>>>>> problems in correctly uploading the data.
>>>>>>> In particular, I get the following error:
>>>>>>>
>>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>>>>>>> Possible problem with experimental design:
>>>>>>> Check for duplicate entries and/or lack of range of continuous
>>>>>>> variables within a class.
>>>>>>> If you seek help with this problem, make sure to send:
>>>>>>> ?This is the command line:
>>>>>>> ?mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh
>>>>>>> --fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods
>>>>>>> --glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage
>>>>>>> lh --label
>>>>>>> /home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C
>>>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
>>>>>>> --C
>>>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat
>>>>>>>
>>>>>>> Of course there is no range for the continuous variable (disease
>>>>>>> duration) in the control group, so I'm wondering how to overcome this
>>>>>>> and generate a?correct qdec.table.dat file.
>>>>>>>
>>>>>>> Thanks in advance for any help!
>>>>>>>
>>>>>>> Pilar
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 7
>>>>>> Date: Mon, 18 Nov 2019 18:30:46 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <ff691f12-1e79-1b2d-463b-3ae47ace83c2@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> I don't understand what you are trying to do. I'm very confused by your
>>>>>> mentioning of bert. What does bert have to do with any of your data?
>>>>>>
>>>>>> On 11/14/19 10:47 AM, An wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Oops sorry for the mistakenly?reply. I will pay more attention in the
>>>>>>> future.
>>>>>>>
>>>>>>> Bert is the folder with the anatomical data. I tried the following
>>>>>>> steps with the 4D volume but failed. Then I checked the registration
>>>>>>> result after bbregister and found that the volume was not registered.
>>>>>>> After that I tried another 4D volume to do the steps and successfully
>>>>>>> got the sampled intensity onto the surface.
>>>>>>>
>>>>>>> The difference between the new 4D volume I used and the previous one
>>>>>>> is that there are two transformation matrices between them. The 4D
>>>>>>> dataset that I previously used but failed is the volume already
>>>>>>> registered to its anatomical volume(by using others tools). The new 4D
>>>>>>> volume that I tried and succeed is the volume not registered.
>>>>>>>
>>>>>>> I have no idea why the 4D volume after the transformation would cause
>>>>>>> a failed result. Could you please let me know that?
>>>>>>>
>>>>>>> Many thanks.
>>>>>>>
>>>>>>> Best,
>>>>>>> An
>>>>>>>
>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?13??? ??12:20???
>>>>>>>
>>>>>>>     If you have an anatomical MR that you have run through recon-all,
>>>>>>>     then
>>>>>>>     just use that one instead of bert in your steps below
>>>>>>>     ps. Please remember to post to the FS list and not to us personally
>>>>>>>
>>>>>>>     On 11/12/19 8:41 PM, an wrote:
>>>>>>>> ????????External Email - Use Caution
>>>>>>>>
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> I got the 4D fMRI dataset from others and it is not raw data. In
>>>>>>>     order
>>>>>>>> to run mri_vol2surf, I need to calculate the register.dat for the
>>>>>>>> required flag --srcreg so I tried in this way.
>>>>>>>>
>>>>>>>> FYI, the 4D fMRI dataset should have been registered with its
>>>>>>>> anatomical MR volume by using other tools.
>>>>>>>>
>>>>>>>> For now I only ran the recon-all on its anatomical MR volume
>>>>>>>     without
>>>>>>>> running the functional stream as I don't have the raw data.
>>>>>>>>
>>>>>>>> Should I also run the raw fMRI data from scratch by using
>>>>>>>     functional
>>>>>>>> stream? Or if I can run mri_vol2surf independently, which command
>>>>>>>> should I use to get a register.dat file?
>>>>>>>> In addition, the intensity of the 4D fMRI dataset I have is between
>>>>>>>> [-1, 1] and not integers, would this cause any problem?
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>>
>>>>>>>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>>> Don't do the 1st step.
>>>>>>>>> Why are you registering it to bert? I'm pretty sure bert did not
>>>>>>>>> participate in your fmri study
>>>>>>>>> When you run mri_vol2surf, it will probably work better with
>>>>>>>>> --projfrac 0.5
>>>>>>>>>
>>>>>>>>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>>>> ????????External Email - Use Caution
>>>>>>>>>>
>>>>>>>>>> Hi Prof. Greve,
>>>>>>>>>>
>>>>>>>>>> Thanks for your reply and sorry for the confusion.
>>>>>>>>>>
>>>>>>>>>> I have a 4D fMRI dataset with 10 time frames, where the
>>>>>>>     intensity of
>>>>>>>>>> each voxel is between [-1,1] and not integers. I want to map the
>>>>>>>>>> intensities of the volumes on its corresponding surface in
>>>>>>>     order to
>>>>>>>>>> get the functional values on each vertex in each frame. I have
>>>>>>>>>> already run its corresponding anatomical image in freesurfer.
>>>>>>>>>>
>>>>>>>>>> To achieve it, I tried the following steps:
>>>>>>>>>> 1. conform the fmri series by using mri_convert
>>>>>>>>>> 2. register the fmri series with the anatomy image by using
>>>>>>>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg
>>>>>>>     register.dat
>>>>>>>>>> 3. assign values from volumes to each vertex by using
>>>>>>>     mri_vol2surf:
>>>>>>>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg
>>>>>>>>>> register.dat --hemi lh
>>>>>>>>>> ? ? I also tried the -regheader in mri_vol2surf: mri_vol2surf
>>>>>>>     --src
>>>>>>>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>     freeview. But
>>>>>>>>>> after step2, the registered volume looks wrong. I am wondering
>>>>>>>     could
>>>>>>>>>> I use bbregister to register multi-frame fMRI series to a single
>>>>>>>>>> volume?
>>>>>>>>>> I also tried to use --regheader to replace the --srcreg file in
>>>>>>>>>> mri_vol2surf as the output register.dat in step2 is wrong. But
>>>>>>>     the
>>>>>>>>>> output is still wrong.
>>>>>>>>>>
>>>>>>>>>> Many thanks.
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>> An
>>>>>>>>>>
>>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>>> ?2019?11?11??? ??12:16???
>>>>>>>>>> ? ? ?When you say it is 4D, what do you mean? That each label
>>>>>>>     has its
>>>>>>>>>> ? ? ?own frame?
>>>>>>>>>>
>>>>>>>>>> ? ? ?On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> ????????External Email - Use Caution
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> Hi there,
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> I am working with creating a surface parcellation from a
>>>>>>>>>> ? ? ?volumetric
>>>>>>>>>> ? ? ?> parcellation and have some questions as follows:
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> 1. If the volumetric parcellation is a labeled 4D
>>>>>>>     multi-frame
>>>>>>>>>> ? ? ?dataset,
>>>>>>>>>> ? ? ?> could I still use the mris_sample_parc? Or could
>>>>>>>     mri_vol2surf
>>>>>>>>>> ? ? ?get the
>>>>>>>>>> ? ? ?> sampled labels for every vertex?
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> 2. For the 4D multi-frame dataset and mri_vol2surf output
>>>>>>>>>> ? ? ?results,
>>>>>>>>>> ? ? ?> which GUI should I use to visualize it? I tried freeview
>>>>>>>     for 4D
>>>>>>>>>> ? ? ?> multi-frame dataset but it looks weird.
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> 3. Is there any command to separate?multi-frame volume to
>>>>>>>>>> ? ? ?single frame
>>>>>>>>>> ? ? ?> volumes?
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> Many thanks!
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> Best,
>>>>>>>>>> ? ? ?> An
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> _______________________________________________
>>>>>>>>>> ? ? ?> Freesurfer mailing list
>>>>>>>>>> ? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>> ? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ?_______________________________________________
>>>>>>>>>> ? ? ?Freesurfer mailing list
>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>> _______________________________________________
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>     The information in this e-mail is intended only for the person to
>>>>>>>     whom it is
>>>>>>>     addressed. If you believe this e-mail was sent to you in error and
>>>>>>>     the e-mail
>>>>>>>     contains patient information, please contact the Partners
>>>>>>>     Compliance HelpLine at
>>>>>>>     http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>>>     you in error
>>>>>>>     but does not contain patient information, please contact the
>>>>>>>     sender and properly
>>>>>>>     dispose of the e-mail.
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 8
>>>>>> Date: Mon, 18 Nov 2019 18:31:35 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] Multiple comparisons
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <745185b7-5ebb-43bf-6d2d-b7328622fe5f@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> My preferred method is to use permutation
>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>>>>>>
>>>>>> On 11/14/19 12:29 PM, Juan Rivas wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> I would like to know how the correction is made for multiple
>>>>>>> comparisons in the statistical analysis? We are using QDEC, with False
>>>>>>> Discovery Rate or Montecarlo Null-Z. Is there a better way to do that?
>>>>>>> Best,
>>>>>>> JC.
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 9
>>>>>> Date: Mon, 18 Nov 2019 18:38:43 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] Questions for PetSurfer
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <f98e29f6-3532-91ed-021f-1e947468f57f@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 11/15/19 4:19 AM, Soo-Jong Kim wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Dear FreeSurfer experts,
>>>>>>>
>>>>>>> I am a student in neuroimaging using FreeSurfer.
>>>>>>> I have some questions and I don't know where to send questions.
>>>>>>> That's why I found this mail and writing.
>>>>>>>
>>>>>>> I've studied PetSurfer for partial volume correction of PET.
>>>>>>> I saw the tutorial in website.
>>>>>>> Originally, I want to use RBV method for pvcorrected PET for SUVR
>>>>>>> analysis.
>>>>>>>
>>>>>>> After generating gtmseg and coregistration to make lta file, I
>>>>>>> followed this code and changed some.
>>>>>>>
>>>>>>> *mri_gtmpvc --i PET.nii --reg subj1.reg.lta --psf 5 --seg gtmseg.mgz *
>>>>>>> *--default-seg-merge --auto-mask PSF .01 --no-rescale --no-reduce-fov
>>>>>>> --rbv --o output_pvc*
>>>>>>>
>>>>>>> After this, rbv.nii.gz file was generated. and SUVR analysis was
>>>>>>> performed as reference region (cerebellar cortex).? But Compared to
>>>>>>> original un-pvc PET, Cortex SUVR was reduced...
>>>>>>>
>>>>>>> In ideal pv-corrected PET, cortex SUVR was higher than?un-pvc PET.
>>>>>>>
>>>>>>> Is is okay if I use the output file as rbv.nii.gz ?
>>>>>> Yes, it does work. Is your tracer one where you expect GM > WM?
>>>>>>> in Thomas et al, 2011,
>>>>>>> He used aparc+aseg.mgz file from FreeSurfer. and he merged some regions.
>>>>>>> Frontal, Temporal, Occipital and so on. (Only gray matter to correct
>>>>>>> PET using RBV method)
>>>>>>>
>>>>>>> In that case, What are the regions to make rbv.nii.gz method in PetSurfer?
>>>>>> Look in aux/seg.ctab (you can visualize the aux/seg.nii.gz)
>>>>>>> Can I use the rbv.nii.gz as partial volume corrected PET from RBV method?
>>>>>> Yes
>>>>>>> If not, Please tell me what is the correct command of mri_gtmpvc.
>>>>>>> I need only partial volume corrected PET using RBV method.
>>>>>>>
>>>>>>> Sincerely,
>>>>>>>
>>>>>>> Soo-Jong Kim
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 10
>>>>>> Date: Mon, 18 Nov 2019 18:39:32 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] Cortical thickness values on a vertex base
>>>>>>   level
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <b9a9830f-fe4d-0321-ede7-1e0a3ee82ca0@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="Windows-1252"
>>>>>>
>>>>>> The sig file
>>>>>>
>>>>>> On 11/15/19 9:16 AM, Aicha Dijkshoorn wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Thank you so much for your repsonse.
>>>>>>> Could you maybe please tell us which input file we should use?
>>>>>>>
>>>>>>> Best wishes,
>>>>>>> AIcha
>>>>>>> ------------------------------------------------------------------------
>>>>>>> *Van:* freesurfer-bounces@nmr.mgh.harvard.edu
>>>>>>> <freesurfer-bounces@nmr.mgh.harvard.edu> namens Greve, Douglas
>>>>>>> N.,Ph.D. <DGREVE@mgh.harvard.edu>
>>>>>>> *Verzonden:* donderdag 31 oktober 2019 19:16
>>>>>>> *Aan:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
>>>>>>> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex
>>>>>>> base level
>>>>>>> You can run mri_surfcluster with your fdr threshold as the --thmin
>>>>>>> value. This will output cluster number (ocn) map. This will assign the
>>>>>>> cluster number to a vertex. You can then use mri_segstats with --seg
>>>>>>> ocn.mgz --excludeid 0 and input being the mean thickness or area maps.
>>>>>>> When you use area as thhe input, make sure to --accumulate to get the
>>>>>>> total area. You can get an area map in the same way that you got the
>>>>>>> thickness map, ie, mris_preproc, etc
>>>>>>>
>>>>>>> On 10/31/19 1:28 PM, Aicha Dijkshoorn wrote:
>>>>>>>> ????????External Email - Use Caution
>>>>>>>>
>>>>>>>> Dear Greve,
>>>>>>>>
>>>>>>>> Thank you for your quick respons.
>>>>>>>>
>>>>>>>> Yes, I believe that is what I mean. Let me illustrate with some
>>>>>>>> (fictive) data;
>>>>>>>> We were able to prove these data for the entire hemisphere as can be
>>>>>>>> seen below.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> *Group 1*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> *Group 2*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> *Difference*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> */Sig./*
>>>>>>>>
>>>>>>>> Thickness
>>>>>>>>
>>>>>>>> (in mm)
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Left
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 1.48
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 1.46
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> .004
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> .19
>>>>>>>>
>>>>>>>> Right
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 1.46
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 1.46
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> .003
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> .03
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> However, we would like to provide similar data in our vertex-base
>>>>>>>> analyses:
>>>>>>>>
>>>>>>>> *Significantly different clusters between group 1 and group 2*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> *Cortical thickness group 1*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> *Cortical thickness group 2*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> *Difference in mm2*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> */Sig./*
>>>>>>>>
>>>>>>>> Left Cuneus
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 0.013
>>>>>>>>
>>>>>>>> Left Fusiform gyrus
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 0.021
>>>>>>>>
>>>>>>>> Right Paracentral lobule
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 0.001
>>>>>>>>
>>>>>>>> Right parahippocampal gyrus
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 0.002
>>>>>>>>
>>>>>>>>
>>>>>>>> Does this clarify my question?
>>>>>>>>
>>>>>>>> Best wishes,
>>>>>>>> Aicha
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> *Van:* freesurfer-bounces@nmr.mgh.harvard.edu
>>>>>>>> <freesurfer-bounces@nmr.mgh.harvard.edu> namens Greve, Douglas
>>>>>>>> N.,Ph.D. <DGREVE@mgh.harvard.edu>
>>>>>>>> *Verzonden:* donderdag 31 oktober 2019 16:25
>>>>>>>> *Aan:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex
>>>>>>>> base level
>>>>>>>> I'm not sure what you mean. Do you want the mean thickness of a cluster
>>>>>>>> and/or its surface area?
>>>>>>>>
>>>>>>>> On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
>>>>>>>>> ????????External Email - Use Caution
>>>>>>>>>
>>>>>>>>> Dear developers,
>>>>>>>>>
>>>>>>>>> For a case-control study we are comparing the cortical thickness and
>>>>>>>>> cortical surface area on a vertex-base level, for which we found
>>>>>>>>> significant differences throughout the brain.
>>>>>>>>>
>>>>>>>>> Is it possible that, in addition to the significance values (p < .05
>>>>>>>>> after FDR correction) on a vertex-base level, we can include the exact
>>>>>>>>> thickness or surface area value (or difference) of the significant
>>>>>>>>> clusters on a vertex base-level between the groups. In order words, to
>>>>>>>>> provide some measures to highlight the size of the significant cluster
>>>>>>>>> or the differences in cortical thickness / cortical surface area to
>>>>>>>>> provide clinically useful context. For instance, a command comparable
>>>>>>>>> to 'voxel size' in TBSS.
>>>>>>>>>
>>>>>>>>> As this is my first time using Freesurfer any help that you could
>>>>>>>>> offer on this matter would be highly appreciated.
>>>>>>>>>
>>>>>>>>> Best wishes,
>>>>>>>>> Brigitte Dijkshoorn
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 11
>>>>>> Date: Mon, 18 Nov 2019 18:41:37 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] Question about the input for longitudinal
>>>>>>   processing pipeline
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <d5205fe6-329a-f9b4-252a-8f1857aa42e4@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> Do all images and time points have contrast? If some do and some don't,
>>>>>> then I don't think you can properly do the analysis?
>>>>>>
>>>>>> On 11/15/19 10:06 AM, Darko Komneni? wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Dear Freesurfer experts,
>>>>>>> I wanted to run the Freesurfer's longitudinal processing pipeline
>>>>>>> (described here
>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) on a
>>>>>>> series of MRI scans from a single patient. However, after looking at
>>>>>>> the scans, i realized that for most time points, the patient doesn't
>>>>>>> have a "simple/normal" T1 MPRAGE sequence available. Instead, they
>>>>>>> have a T1 sequence with a contrast agent, as well as T1 mp2rage
>>>>>>> sequences.
>>>>>>>
>>>>>>> Is it possible/advisable to run recon-all in general or this pipeline
>>>>>>> in particular on T1 MPRAGE scans that have a contrast agent, or that
>>>>>>> are mp2rage instead of MPRAGE?
>>>>>>>
>>>>>>> Thanks in advance!
>>>>>>> Best,
>>>>>>> Darko
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 12
>>>>>> Date: Mon, 18 Nov 2019 18:45:17 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] Brain lobules pooling- request
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <a457c4e8-913e-706e-c7ef-8925c7eaad3d@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="Windows-1252"
>>>>>>
>>>>>> sorry, it is not clear to me what is going wrong here. Did the
>>>>>> mri_annotation2label command fail? or mris_anatomical_stats command?
>>>>>>
>>>>>> On 11/17/19 9:55 PM, Samson Nivins wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Hi FreeSurfer Team,
>>>>>>>
>>>>>>> ????? I am interested in individual lobular volume and thickness. So I
>>>>>>> have extracted based on the Q and A I created few script to run and
>>>>>>> extract the data.
>>>>>>>
>>>>>>> However, I got few questions regarding thickness and WM
>>>>>>>
>>>>>>> For extracting lobular GM I used
>>>>>>>
>>>>>>> mri_annotation2label --subject 1014? --hemi lh --lobesStrict
>>>>>>> lh.lobesStrict.annot
>>>>>>>
>>>>>>> mri_annotation2label --subject 1014? --hemi lh --annotation
>>>>>>> lobesStrict --outdir
>>>>>>> '/home/samson/Volume/freesurfer/subjects/recon-all_working/lh'
>>>>>>>
>>>>>>> for computing stats I used
>>>>>>>
>>>>>>> mris_anatomical_stats -l
>>>>>>> '/home/samson/Volume/freesurfer/subjects/recon-all_working/lh/lh.occipital.label'
>>>>>>> -b 1014 lh
>>>>>>>
>>>>>>> I am not sure, whether any command is there to export the data.
>>>>>>>
>>>>>>> And, the average cortical thickness which we obtain in the terminal
>>>>>>> window during individual extraction, does it correspond to the lobular
>>>>>>> thickness or as whole
>>>>>>>
>>>>>>> For example
>>>>>>>
>>>>>>> I extracted stats for left frontal cortex:
>>>>>>>
>>>>>>> I got the following details in Terminal window
>>>>>>>
>>>>>>> Number of vertices, Total surface area, total gray matter, average
>>>>>>> cortical thickness ?.
>>>>>>>
>>>>>>> In this average cortical thickness ? correspond to the ROI specifc are
>>>>>>> as a whole?
>>>>>>>
>>>>>>> Thanks for you help.
>>>>>>>
>>>>>>> Looking forward to hearing from you
>>>>>>>
>>>>>>> Cheers
>>>>>>>
>>>>>>> Best regards,
>>>>>>>
>>>>>>> Sam
>>>>>>>
>>>>>>> *Samson Nivins? |**PhD Student*
>>>>>>>
>>>>>>> **
>>>>>>>
>>>>>>> *A*The University of Auckland, Liggins Institute
>>>>>>>
>>>>>>> Building 505, Level 2, 85 Park Road, Auckland
>>>>>>>
>>>>>>> *Ph *+(64) 21 256 5964
>>>>>>>
>>>>>>> *E*samson.nivins@gmail.com <mailto:samson.nivins@gmail.com>
>>>>>>>
>>>>>>> *//*
>>>>>>>
>>>>>>> cid:image001.png@01D4C1F6.9273DF90
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 13
>>>>>> Date: Mon, 18 Nov 2019 13:48:58 -0500
>>>>>> From: An <annaqu1024@gmail.com>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <CAJVCUNcDB0ggDRvgbBVYBzftLTdQ42jvUhGhO0+UKe+tkniRoA@mail.gmail.com>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>         External Email - Use Caution
>>>>>>
>>>>>> I want to map the intensities of the volumes on its corresponding surface
>>>>>> in order to get the functional values on each vertex in each frame. I ran
>>>>>> recon-all for the anatomical volume and saved all outputs(mri,labels,surf
>>>>>> and etc.) in the bert folder. I use it because I need to specify the
>>>>>> required flag -s in bbregister in order to register the functional volume
>>>>>> to its anatomical volume.
>>>>>>
>>>>>> Many thanks.
>>>>>>
>>>>>> Best,
>>>>>> An
>>>>>>
>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> ?2019?11?18??? ??1:31???
>>>>>>
>>>>>>> I don't understand what you are trying to do. I'm very confused by your
>>>>>>> mentioning of bert. What does bert have to do with any of your data?
>>>>>>>
>>>>>>> On 11/14/19 10:47 AM, An wrote:
>>>>>>>>         External Email - Use Caution
>>>>>>>>
>>>>>>>> Oops sorry for the mistakenly reply. I will pay more attention in the
>>>>>>>> future.
>>>>>>>>
>>>>>>>> Bert is the folder with the anatomical data. I tried the following
>>>>>>>> steps with the 4D volume but failed. Then I checked the registration
>>>>>>>> result after bbregister and found that the volume was not registered.
>>>>>>>> After that I tried another 4D volume to do the steps and successfully
>>>>>>>> got the sampled intensity onto the surface.
>>>>>>>>
>>>>>>>> The difference between the new 4D volume I used and the previous one
>>>>>>>> is that there are two transformation matrices between them. The 4D
>>>>>>>> dataset that I previously used but failed is the volume already
>>>>>>>> registered to its anatomical volume(by using others tools). The new 4D
>>>>>>>> volume that I tried and succeed is the volume not registered.
>>>>>>>>
>>>>>>>> I have no idea why the 4D volume after the transformation would cause
>>>>>>>> a failed result. Could you please let me know that?
>>>>>>>>
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?13??? ??12:20???
>>>>>>>>
>>>>>>>>     If you have an anatomical MR that you have run through recon-all,
>>>>>>>>     then
>>>>>>>>     just use that one instead of bert in your steps below
>>>>>>>>     ps. Please remember to post to the FS list and not to us personally
>>>>>>>>
>>>>>>>>     On 11/12/19 8:41 PM, an wrote:
>>>>>>>>>         External Email - Use Caution
>>>>>>>>>
>>>>>>>>> Many thanks.
>>>>>>>>>
>>>>>>>>> I got the 4D fMRI dataset from others and it is not raw data. In
>>>>>>>>     order
>>>>>>>>> to run mri_vol2surf, I need to calculate the register.dat for the
>>>>>>>>> required flag --srcreg so I tried in this way.
>>>>>>>>>
>>>>>>>>> FYI, the 4D fMRI dataset should have been registered with its
>>>>>>>>> anatomical MR volume by using other tools.
>>>>>>>>>
>>>>>>>>> For now I only ran the recon-all on its anatomical MR volume
>>>>>>>>     without
>>>>>>>>> running the functional stream as I don't have the raw data.
>>>>>>>>>
>>>>>>>>> Should I also run the raw fMRI data from scratch by using
>>>>>>>>     functional
>>>>>>>>> stream? Or if I can run mri_vol2surf independently, which command
>>>>>>>>> should I use to get a register.dat file?
>>>>>>>>> In addition, the intensity of the 4D fMRI dataset I have is between
>>>>>>>>> [-1, 1] and not integers, would this cause any problem?
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> An
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>>>> Don't do the 1st step.
>>>>>>>>>> Why are you registering it to bert? I'm pretty sure bert did not
>>>>>>>>>> participate in your fmri study
>>>>>>>>>> When you run mri_vol2surf, it will probably work better with
>>>>>>>>>> --projfrac 0.5
>>>>>>>>>>
>>>>>>>>>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>>>>>         External Email - Use Caution
>>>>>>>>>>>
>>>>>>>>>>> Hi Prof. Greve,
>>>>>>>>>>>
>>>>>>>>>>> Thanks for your reply and sorry for the confusion.
>>>>>>>>>>>
>>>>>>>>>>> I have a 4D fMRI dataset with 10 time frames, where the
>>>>>>>>     intensity of
>>>>>>>>>>> each voxel is between [-1,1] and not integers. I want to map the
>>>>>>>>>>> intensities of the volumes on its corresponding surface in
>>>>>>>>     order to
>>>>>>>>>>> get the functional values on each vertex in each frame. I have
>>>>>>>>>>> already run its corresponding anatomical image in freesurfer.
>>>>>>>>>>>
>>>>>>>>>>> To achieve it, I tried the following steps:
>>>>>>>>>>> 1. conform the fmri series by using mri_convert
>>>>>>>>>>> 2. register the fmri series with the anatomy image by using
>>>>>>>>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg
>>>>>>>>     register.dat
>>>>>>>>>>> 3. assign values from volumes to each vertex by using
>>>>>>>>     mri_vol2surf:
>>>>>>>>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg
>>>>>>>>>>> register.dat --hemi lh
>>>>>>>>>>>     I also tried the -regheader in mri_vol2surf: mri_vol2surf
>>>>>>>>     --src
>>>>>>>>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>>     freeview. But
>>>>>>>>>>> after step2, the registered volume looks wrong. I am wondering
>>>>>>>>     could
>>>>>>>>>>> I use bbregister to register multi-frame fMRI series to a single
>>>>>>>>>>> volume?
>>>>>>>>>>> I also tried to use --regheader to replace the --srcreg file in
>>>>>>>>>>> mri_vol2surf as the output register.dat in step2 is wrong. But
>>>>>>>>     the
>>>>>>>>>>> output is still wrong.
>>>>>>>>>>>
>>>>>>>>>>> Many thanks.
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>> An
>>>>>>>>>>>
>>>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>>> ?2019?11?11??? ??12:16???
>>>>>>>>>>>     When you say it is 4D, what do you mean? That each label
>>>>>>>>     has its
>>>>>>>>>>>     own frame?
>>>>>>>>>>>
>>>>>>>>>>>     On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>>>>>>         External Email - Use Caution
>>>>>>>>>>>>
>>>>>>>>>>>> Hi there,
>>>>>>>>>>>>
>>>>>>>>>>>> I am working with creating a surface parcellation from a
>>>>>>>>>>>     volumetric
>>>>>>>>>>>> parcellation and have some questions as follows:
>>>>>>>>>>>>
>>>>>>>>>>>> 1. If the volumetric parcellation is a labeled 4D
>>>>>>>>     multi-frame
>>>>>>>>>>>     dataset,
>>>>>>>>>>>> could I still use the mris_sample_parc? Or could
>>>>>>>>     mri_vol2surf
>>>>>>>>>>>     get the
>>>>>>>>>>>> sampled labels for every vertex?
>>>>>>>>>>>>
>>>>>>>>>>>> 2. For the 4D multi-frame dataset and mri_vol2surf output
>>>>>>>>>>>     results,
>>>>>>>>>>>> which GUI should I use to visualize it? I tried freeview
>>>>>>>>     for 4D
>>>>>>>>>>>> multi-frame dataset but it looks weird.
>>>>>>>>>>>>
>>>>>>>>>>>> 3. Is there any command to separate multi-frame volume to
>>>>>>>>>>>     single frame
>>>>>>>>>>>> volumes?
>>>>>>>>>>>>
>>>>>>>>>>>> Many thanks!
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Best,
>>>>>>>>>>>> An
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>     Freesurfer mailing list
>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>     The information in this e-mail is intended only for the person to
>>>>>>>>     whom it is
>>>>>>>>     addressed. If you believe this e-mail was sent to you in error and
>>>>>>>>     the e-mail
>>>>>>>>     contains patient information, please contact the Partners
>>>>>>>>     Compliance HelpLine at
>>>>>>>>     http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>>>>     you in error
>>>>>>>>     but does not contain patient information, please contact the
>>>>>>>>     sender and properly
>>>>>>>>     dispose of the e-mail.
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> -------------- next part --------------
>>>>>> An HTML attachment was scrubbed...
>>>>>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191118/109d956d/attachment-0001.html
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 14
>>>>>> Date: Mon, 18 Nov 2019 19:27:31 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] (no subject)
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <bc2fb054-9b5d-938d-a2ea-5fafb4a27d5c@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> It gets the subcortical from apas+head.mgz which gets created along the
>>>>>> way by xcerebralseg. You can create your own with xcerebralseg by
>>>>>> specifying your volume as the mergevol. I think this will work, but I'm
>>>>>> not sure. I'm assuming you've used the GCA to create your own
>>>>>> subcortical seg for the given subject
>>>>>>
>>>>>> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> I just realized that the above?mentioned command (gtmseg --s XYZ --o
>>>>>>> BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
>>>>>>> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg)
>>>>>>> gives me only the cortical segmentation. Is there any way to also
>>>>>>> include the subcortical segmentation based on my individual atlas? I
>>>>>>> also have an Atlas_subcortex.gca file available.
>>>>>>>
>>>>>>> Best,
>>>>>>> Boris
>>>>>>>
>>>>>>> On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
>>>>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>>>>>>>
>>>>>>>     There is no cut off for the minimum size. As it gets smaller, the PVC
>>>>>>>     noise amplification will become bigger (it also depends on the
>>>>>>>     shape as
>>>>>>>     well).
>>>>>>>
>>>>>>>     I think the --no-xcerseg is the right way to go now
>>>>>>>
>>>>>>>     On 8/13/19 11:00 AM, Boris Rauchmann wrote:
>>>>>>>> ????????External Email - Use Caution
>>>>>>>>
>>>>>>>> Thank you for your prompt answer - the command worked. This is the
>>>>>>>> atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
>>>>>>>> What is approximately the smallest possible segment when using PVC?
>>>>>>>> Also, does the exclusion of extracerebral structures harm? I
>>>>>>>     used that
>>>>>>>> flag because it complained:
>>>>>>>>
>>>>>>>> gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
>>>>>>>> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
>>>>>>>> ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
>>>>>>>> but you must indicate whether to use what is there (--no-xcerseg)
>>>>>>>> or create a new one and overwrite what is there (--xcerseg)
>>>>>>>> or specify your own headseg (--head)
>>>>>>>>
>>>>>>>> and did not want to override my apas+head.mgz
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Boris
>>>>>>>>
>>>>>>>> On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
>>>>>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>     wrote:
>>>>>>>> ? ? ?I don't know what the Brainnetome is, but it looks like you have
>>>>>>>> ? ? ?it in
>>>>>>>> ? ? ?annotation form. I think that command should work. Why are
>>>>>>>     you using
>>>>>>>> ? ? ?--no-xcerseg? This will cause it to not include extracerebral
>>>>>>>> ? ? ?structures. Also note that you cannot use arbitrarily small
>>>>>>>     segments
>>>>>>>> ? ? ?when doing PVC.
>>>>>>>>
>>>>>>>> ? ? ?On 8/13/19 10:26 AM, Boris Rauchmann wrote:
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Dear all,
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> my intention is to use the Brainnetome Atlas
>>>>>>>> ? ? ?parcellation/segmentation
>>>>>>>> ? ? ?> in PETSurfer to obtain PVC corrected SUVRs for the atlas
>>>>>>>     ROIs. I
>>>>>>>> ? ? ?used:
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot
>>>>>>>     BN_Atlas.annot --ctab
>>>>>>>> ? ? ?> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
>>>>>>>     --no-xcerseg
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Is this the right approach to obtain a high resolution
>>>>>>>> ? ? ?segmentation to
>>>>>>>> ? ? ?> run PVC methods?
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Thanks,
>>>>>>>> ? ? ?> Boris
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> _______________________________________________
>>>>>>>> ? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> ? ? ?_______________________________________________
>>>>>>>> ? ? ?Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>     _______________________________________________
>>>>>>>     Freesurfer mailing list
>>>>>>>     Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 15
>>>>>> Date: Mon, 18 Nov 2019 19:32:49 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <7d550731-08c1-d66c-5dca-d14bb313ba5c@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> What was your original recon-all command?
>>>>>>
>>>>>> On 11/18/19 1:48 PM, An wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> I want to map the intensities of the volumes on its corresponding
>>>>>>> surface in order to get the functional values on each vertex in each
>>>>>>> frame.?I ran recon-all for the anatomical volume and saved all
>>>>>>> outputs(mri,labels,surf and etc.) in the bert folder. I use it because
>>>>>>> I need to specify?the required flag -s in bbregister in order to
>>>>>>> register the functional volume to its anatomical volume.
>>>>>>>
>>>>>>> Many thanks.
>>>>>>>
>>>>>>> Best,
>>>>>>> An
>>>>>>>
>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?18??? ??1:31???
>>>>>>>
>>>>>>>     I don't understand what you are trying to do. I'm very confused by
>>>>>>>     your
>>>>>>>     mentioning of bert. What does bert have to do with any of your data?
>>>>>>>
>>>>>>>     On 11/14/19 10:47 AM, An wrote:
>>>>>>>> ????????External Email - Use Caution
>>>>>>>>
>>>>>>>> Oops sorry for the mistakenly?reply. I will pay more attention
>>>>>>>     in the
>>>>>>>> future.
>>>>>>>>
>>>>>>>> Bert is the folder with the anatomical data. I tried the following
>>>>>>>> steps with the 4D volume but failed. Then I checked the
>>>>>>>     registration
>>>>>>>> result after bbregister and found that the volume was not
>>>>>>>     registered.
>>>>>>>> After that I tried another 4D volume to do the steps and
>>>>>>>     successfully
>>>>>>>> got the sampled intensity onto the surface.
>>>>>>>>
>>>>>>>> The difference between the new 4D volume I used and the previous
>>>>>>>     one
>>>>>>>> is that there are two transformation matrices between them. The 4D
>>>>>>>> dataset that I previously used but failed is the volume already
>>>>>>>> registered to its anatomical volume(by using others tools). The
>>>>>>>     new 4D
>>>>>>>> volume that I tried and succeed is the volume not registered.
>>>>>>>>
>>>>>>>> I have no idea why the 4D volume after the transformation would
>>>>>>>     cause
>>>>>>>> a failed result. Could you please let me know that?
>>>>>>>>
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>     ?2019?11?13??? ??12:20???
>>>>>>>> ? ? ?If you have an anatomical MR that you have run through
>>>>>>>     recon-all,
>>>>>>>> ? ? ?then
>>>>>>>> ? ? ?just use that one instead of bert in your steps below
>>>>>>>> ? ? ?ps. Please remember to post to the FS list and not to us
>>>>>>>     personally
>>>>>>>> ? ? ?On 11/12/19 8:41 PM, an wrote:
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Many thanks.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> I got the 4D fMRI dataset from others and it is not raw
>>>>>>>     data. In
>>>>>>>> ? ? ?order
>>>>>>>> ? ? ?> to run mri_vol2surf, I need to calculate the register.dat
>>>>>>>     for the
>>>>>>>> ? ? ?> required flag --srcreg so I tried in this way.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> FYI, the 4D fMRI dataset should have been registered with its
>>>>>>>> ? ? ?> anatomical MR volume by using other tools.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> For now I only ran the recon-all on its anatomical MR volume
>>>>>>>> ? ? ?without
>>>>>>>> ? ? ?> running the functional stream as I don't have the raw data.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Should I also run the raw fMRI data from scratch by using
>>>>>>>> ? ? ?functional
>>>>>>>> ? ? ?> stream? Or if I can run mri_vol2surf independently, which
>>>>>>>     command
>>>>>>>> ? ? ?> should I use to get a register.dat file?
>>>>>>>> ? ? ?> In addition, the intensity of the 4D fMRI dataset I have
>>>>>>>     is between
>>>>>>>> ? ? ?> [-1, 1] and not integers, would this cause any problem?
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Best,
>>>>>>>> ? ? ?> An
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>> ? ? ?>> Don't do the 1st step.
>>>>>>>> ? ? ?>> Why are you registering it to bert? I'm pretty sure bert
>>>>>>>     did not
>>>>>>>> ? ? ?>> participate in your fmri study
>>>>>>>> ? ? ?>> When you run mri_vol2surf, it will probably work better with
>>>>>>>> ? ? ?>> --projfrac 0.5
>>>>>>>> ? ? ?>>
>>>>>>>> ? ? ?>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> ????????External Email - Use Caution
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> Hi Prof. Greve,
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> Thanks for your reply and sorry for the confusion.
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> I have a 4D fMRI dataset with 10 time frames, where the
>>>>>>>> ? ? ?intensity of
>>>>>>>> ? ? ?>>> each voxel is between [-1,1] and not integers. I want to
>>>>>>>     map the
>>>>>>>> ? ? ?>>> intensities of the volumes on its corresponding surface in
>>>>>>>> ? ? ?order to
>>>>>>>> ? ? ?>>> get the functional values on each vertex in each frame.
>>>>>>>     I have
>>>>>>>> ? ? ?>>> already run its corresponding anatomical image in
>>>>>>>     freesurfer.
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> To achieve it, I tried the following steps:
>>>>>>>> ? ? ?>>> 1. conform the fmri series by using mri_convert
>>>>>>>> ? ? ?>>> 2. register the fmri series with the anatomy image by using
>>>>>>>> ? ? ?>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg
>>>>>>>> ? ? ?register.dat
>>>>>>>> ? ? ?>>> 3. assign values from volumes to each vertex by using
>>>>>>>> ? ? ?mri_vol2surf:
>>>>>>>> ? ? ?>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg
>>>>>>>> ? ? ?>>> register.dat --hemi lh
>>>>>>>> ? ? ?>>> ? ? I also tried the -regheader in mri_vol2surf:
>>>>>>>     mri_vol2surf
>>>>>>>> ? ? ?--src
>>>>>>>> ? ? ?>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>> ? ? ?freeview. But
>>>>>>>> ? ? ?>>> after step2, the registered volume looks wrong. I am
>>>>>>>     wondering
>>>>>>>> ? ? ?could
>>>>>>>> ? ? ?>>> I use bbregister to register multi-frame fMRI series to
>>>>>>>     a single
>>>>>>>> ? ? ?>>> volume?
>>>>>>>> ? ? ?>>> I also tried to use --regheader to replace the --srcreg
>>>>>>>     file in
>>>>>>>> ? ? ?>>> mri_vol2surf as the output register.dat in step2 is
>>>>>>>     wrong. But
>>>>>>>> ? ? ?the
>>>>>>>> ? ? ?>>> output is still wrong.
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> Many thanks.
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> Best,
>>>>>>>> ? ? ?>>> An
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>>>> ?2019?11?11???
>>>>>>>     ??12:16???
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>>? ? ?When you say it is 4D, what do you mean? That each label
>>>>>>>> ? ? ?has its
>>>>>>>> ? ? ?>>>? ? ?own frame?
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>>? ? ?On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> Hi there,
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> I am working with creating a surface parcellation
>>>>>>>     from a
>>>>>>>> ? ? ?>>>? ? ?volumetric
>>>>>>>> ? ? ?>>>? ? ?> parcellation and have some questions as follows:
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> 1. If the volumetric parcellation is a labeled 4D
>>>>>>>> ? ? ?multi-frame
>>>>>>>> ? ? ?>>>? ? ?dataset,
>>>>>>>> ? ? ?>>>? ? ?> could I still use the mris_sample_parc? Or could
>>>>>>>> ? ? ?mri_vol2surf
>>>>>>>> ? ? ?>>>? ? ?get the
>>>>>>>> ? ? ?>>>? ? ?> sampled labels for every vertex?
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> 2. For the 4D multi-frame dataset and mri_vol2surf
>>>>>>>     output
>>>>>>>> ? ? ?>>>? ? ?results,
>>>>>>>> ? ? ?>>>? ? ?> which GUI should I use to visualize it? I tried
>>>>>>>     freeview
>>>>>>>> ? ? ?for 4D
>>>>>>>> ? ? ?>>>? ? ?> multi-frame dataset but it looks weird.
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> 3. Is there any command to separate?multi-frame
>>>>>>>     volume to
>>>>>>>> ? ? ?>>>? ? ?single frame
>>>>>>>> ? ? ?>>>? ? ?> volumes?
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> Many thanks!
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> Best,
>>>>>>>> ? ? ?>>>? ? ?> An
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> _______________________________________________
>>>>>>>> ? ? ?>>>? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?>>>? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>>>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> ?_______________________________________________
>>>>>>>> ? ? ?>>>? ? ?Freesurfer mailing list
>>>>>>>> ? ? ?>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>>>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> _______________________________________________
>>>>>>>> ? ? ?>>> Freesurfer mailing list
>>>>>>>> ? ? ?>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>>
>>>>>>>> ? ? ?>>
>>>>>>>> ? ? ?>> _______________________________________________
>>>>>>>> ? ? ?>> Freesurfer mailing list
>>>>>>>> ? ? ?>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ? ? ?The information in this e-mail is intended only for the
>>>>>>>     person to
>>>>>>>> ? ? ?whom it is
>>>>>>>> ? ? ?addressed. If you believe this e-mail was sent to you in
>>>>>>>     error and
>>>>>>>> ? ? ?the e-mail
>>>>>>>> ? ? ?contains patient information, please contact the Partners
>>>>>>>> ? ? ?Compliance HelpLine at
>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>>>> ? ? ?you in error
>>>>>>>> ? ? ?but does not contain patient information, please contact the
>>>>>>>> ? ? ?sender and properly
>>>>>>>> ? ? ?dispose of the e-mail.
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>     _______________________________________________
>>>>>>>     Freesurfer mailing list
>>>>>>>     Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 16
>>>>>> Date: Mon, 18 Nov 2019 14:53:24 -0500
>>>>>> From: An <annaqu1024@gmail.com>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <CAJVCUNfyc63KvvwVCuzw6EPVNVhbr0fSYs3m_2hP9-48OyA-ag@mail.gmail.com>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>         External Email - Use Caution
>>>>>>
>>>>>> Here is my recon-all command line:
>>>>>>
>>>>>> recon-all -i ana_Vol.nii -s bert -all
>>>>>>
>>>>>> Many thanks.
>>>>>>
>>>>>> Best,
>>>>>> An
>>>>>>
>>>>>>
>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> ?2019?11?18??? ??2:33???
>>>>>>
>>>>>>> What was your original recon-all command?
>>>>>>>
>>>>>>> On 11/18/19 1:48 PM, An wrote:
>>>>>>>>         External Email - Use Caution
>>>>>>>>
>>>>>>>> I want to map the intensities of the volumes on its corresponding
>>>>>>>> surface in order to get the functional values on each vertex in each
>>>>>>>> frame. I ran recon-all for the anatomical volume and saved all
>>>>>>>> outputs(mri,labels,surf and etc.) in the bert folder. I use it because
>>>>>>>> I need to specify the required flag -s in bbregister in order to
>>>>>>>> register the functional volume to its anatomical volume.
>>>>>>>>
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?18??? ??1:31???
>>>>>>>>
>>>>>>>>     I don't understand what you are trying to do. I'm very confused by
>>>>>>>>     your
>>>>>>>>     mentioning of bert. What does bert have to do with any of your data?
>>>>>>>>
>>>>>>>>     On 11/14/19 10:47 AM, An wrote:
>>>>>>>>>         External Email - Use Caution
>>>>>>>>>
>>>>>>>>> Oops sorry for the mistakenly reply. I will pay more attention
>>>>>>>>     in the
>>>>>>>>> future.
>>>>>>>>>
>>>>>>>>> Bert is the folder with the anatomical data. I tried the following
>>>>>>>>> steps with the 4D volume but failed. Then I checked the
>>>>>>>>     registration
>>>>>>>>> result after bbregister and found that the volume was not
>>>>>>>>     registered.
>>>>>>>>> After that I tried another 4D volume to do the steps and
>>>>>>>>     successfully
>>>>>>>>> got the sampled intensity onto the surface.
>>>>>>>>>
>>>>>>>>> The difference between the new 4D volume I used and the previous
>>>>>>>>     one
>>>>>>>>> is that there are two transformation matrices between them. The 4D
>>>>>>>>> dataset that I previously used but failed is the volume already
>>>>>>>>> registered to its anatomical volume(by using others tools). The
>>>>>>>>     new 4D
>>>>>>>>> volume that I tried and succeed is the volume not registered.
>>>>>>>>>
>>>>>>>>> I have no idea why the 4D volume after the transformation would
>>>>>>>>     cause
>>>>>>>>> a failed result. Could you please let me know that?
>>>>>>>>>
>>>>>>>>> Many thanks.
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> An
>>>>>>>>>
>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>>     ?2019?11?13??? ??12:20???
>>>>>>>>>     If you have an anatomical MR that you have run through
>>>>>>>>     recon-all,
>>>>>>>>>     then
>>>>>>>>>     just use that one instead of bert in your steps below
>>>>>>>>>     ps. Please remember to post to the FS list and not to us
>>>>>>>>     personally
>>>>>>>>>     On 11/12/19 8:41 PM, an wrote:
>>>>>>>>>>         External Email - Use Caution
>>>>>>>>>>
>>>>>>>>>> Many thanks.
>>>>>>>>>>
>>>>>>>>>> I got the 4D fMRI dataset from others and it is not raw
>>>>>>>>     data. In
>>>>>>>>>     order
>>>>>>>>>> to run mri_vol2surf, I need to calculate the register.dat
>>>>>>>>     for the
>>>>>>>>>> required flag --srcreg so I tried in this way.
>>>>>>>>>>
>>>>>>>>>> FYI, the 4D fMRI dataset should have been registered with its
>>>>>>>>>> anatomical MR volume by using other tools.
>>>>>>>>>>
>>>>>>>>>> For now I only ran the recon-all on its anatomical MR volume
>>>>>>>>>     without
>>>>>>>>>> running the functional stream as I don't have the raw data.
>>>>>>>>>>
>>>>>>>>>> Should I also run the raw fMRI data from scratch by using
>>>>>>>>>     functional
>>>>>>>>>> stream? Or if I can run mri_vol2surf independently, which
>>>>>>>>     command
>>>>>>>>>> should I use to get a register.dat file?
>>>>>>>>>> In addition, the intensity of the 4D fMRI dataset I have
>>>>>>>>     is between
>>>>>>>>>> [-1, 1] and not integers, would this cause any problem?
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>> An
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>>>>> Don't do the 1st step.
>>>>>>>>>>> Why are you registering it to bert? I'm pretty sure bert
>>>>>>>>     did not
>>>>>>>>>>> participate in your fmri study
>>>>>>>>>>> When you run mri_vol2surf, it will probably work better with
>>>>>>>>>>> --projfrac 0.5
>>>>>>>>>>>
>>>>>>>>>>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>>>>>>         External Email - Use Caution
>>>>>>>>>>>>
>>>>>>>>>>>> Hi Prof. Greve,
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks for your reply and sorry for the confusion.
>>>>>>>>>>>>
>>>>>>>>>>>> I have a 4D fMRI dataset with 10 time frames, where the
>>>>>>>>>     intensity of
>>>>>>>>>>>> each voxel is between [-1,1] and not integers. I want to
>>>>>>>>     map the
>>>>>>>>>>>> intensities of the volumes on its corresponding surface in
>>>>>>>>>     order to
>>>>>>>>>>>> get the functional values on each vertex in each frame.
>>>>>>>>     I have
>>>>>>>>>>>> already run its corresponding anatomical image in
>>>>>>>>     freesurfer.
>>>>>>>>>>>> To achieve it, I tried the following steps:
>>>>>>>>>>>> 1. conform the fmri series by using mri_convert
>>>>>>>>>>>> 2. register the fmri series with the anatomy image by using
>>>>>>>>>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg
>>>>>>>>>     register.dat
>>>>>>>>>>>> 3. assign values from volumes to each vertex by using
>>>>>>>>>     mri_vol2surf:
>>>>>>>>>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg
>>>>>>>>>>>> register.dat --hemi lh
>>>>>>>>>>>>     I also tried the -regheader in mri_vol2surf:
>>>>>>>>     mri_vol2surf
>>>>>>>>>     --src
>>>>>>>>>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>>>     freeview. But
>>>>>>>>>>>> after step2, the registered volume looks wrong. I am
>>>>>>>>     wondering
>>>>>>>>>     could
>>>>>>>>>>>> I use bbregister to register multi-frame fMRI series to
>>>>>>>>     a single
>>>>>>>>>>>> volume?
>>>>>>>>>>>> I also tried to use --regheader to replace the --srcreg
>>>>>>>>     file in
>>>>>>>>>>>> mri_vol2surf as the output register.dat in step2 is
>>>>>>>>     wrong. But
>>>>>>>>>     the
>>>>>>>>>>>> output is still wrong.
>>>>>>>>>>>>
>>>>>>>>>>>> Many thanks.
>>>>>>>>>>>>
>>>>>>>>>>>> Best,
>>>>>>>>>>>> An
>>>>>>>>>>>>
>>>>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>>
>>>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>>>> ?2019?11?11???
>>>>>>>>     ??12:16???
>>>>>>>>>>>>     When you say it is 4D, what do you mean? That each
>>>>>>> label
>>>>>>>>>     has its
>>>>>>>>>>>>     own frame?
>>>>>>>>>>>>
>>>>>>>>>>>>     On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>>>>>>>         External Email - Use Caution
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hi there,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I am working with creating a surface parcellation
>>>>>>>>     from a
>>>>>>>>>>>>     volumetric
>>>>>>>>>>>>> parcellation and have some questions as follows:
>>>>>>>>>>>>>
>>>>>>>>>>>>> 1. If the volumetric parcellation is a labeled 4D
>>>>>>>>>     multi-frame
>>>>>>>>>>>>     dataset,
>>>>>>>>>>>>> could I still use the mris_sample_parc? Or could
>>>>>>>>>     mri_vol2surf
>>>>>>>>>>>>     get the
>>>>>>>>>>>>> sampled labels for every vertex?
>>>>>>>>>>>>>
>>>>>>>>>>>>> 2. For the 4D multi-frame dataset and mri_vol2surf
>>>>>>>>     output
>>>>>>>>>>>>     results,
>>>>>>>>>>>>> which GUI should I use to visualize it? I tried
>>>>>>>>     freeview
>>>>>>>>>     for 4D
>>>>>>>>>>>>> multi-frame dataset but it looks weird.
>>>>>>>>>>>>>
>>>>>>>>>>>>> 3. Is there any command to separate multi-frame
>>>>>>>>     volume to
>>>>>>>>>>>>     single frame
>>>>>>>>>>>>> volumes?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Many thanks!
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Best,
>>>>>>>>>>>>> An
>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>     Freesurfer mailing list
>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>     The information in this e-mail is intended only for the
>>>>>>>>     person to
>>>>>>>>>     whom it is
>>>>>>>>>     addressed. If you believe this e-mail was sent to you in
>>>>>>>>     error and
>>>>>>>>>     the e-mail
>>>>>>>>>     contains patient information, please contact the Partners
>>>>>>>>>     Compliance HelpLine at
>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>>>>>     you in error
>>>>>>>>>     but does not contain patient information, please contact the
>>>>>>>>>     sender and properly
>>>>>>>>>     dispose of the e-mail.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>     _______________________________________________
>>>>>>>>     Freesurfer mailing list
>>>>>>>>     Freesurfer@nmr.mgh.harvard.edu <mailto:
>>>>>>> Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> -------------- next part --------------
>>>>>> An HTML attachment was scrubbed...
>>>>>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191118/e0d70211/attachment-0001.html
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 17
>>>>>> Date: Mon, 18 Nov 2019 16:07:40 -0500
>>>>>> From: Vinny K <vinit.k.srivastava@gmail.com>
>>>>>> Subject: Re: [Freesurfer] use of .m3z transform output from
>>>>>>   mri_cvs_register
>>>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <CACUgD2xDPEaoEO6SfJMemQ5On_tTWy=K-r4+_QgXRSQTO7avzA@mail.gmail.com>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>         External Email - Use Caution
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I had mistakenly used the raw moving image in the mri_convert command.  It
>>>>>> should have been the norm.mgz from the moving subject.  The output image
>>>>>> from the mri_convert command now perfectly overlaps with the output from
>>>>>> mri_cvs_register.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Vinny
>>>>>>
>>>>>> On Sat, Nov 16, 2019 at 4:56 PM Vinny K <vinit.k.srivastava@gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I ran the mri_cvs_register between two subjectIDs with very good alignment

>>>>>>> between them.  I had assumed that applying the outputted m3z transform,
>>>>>>> i.e.,final _CVSmorph_toTEMPLATE.m3z, to the moving subjectID (subjb)
>>>>>>> would normalize it to the target subjectID (subja).  That is, the outputted
>>>>>>> image would be the same as the output image from mri_cvs_register
>>>>>>> ,final_CVSmorphed_toTEMPLAT_norm.mgz; however, the resulting image was
>>>>>>> totally out of alignment to the target subjectID.  This is the command I
>>>>>>> had utilized to apply the m3z transform to the moving subjectID:
>>>>>>>
>>>>>>> mri_convert -at
>>>>>>> /home/vinny/Tools/freesurfer/subjects/subjb/cvs/final_CVSmorph_tosubja.m3z
>>>>>>> subjb.nii.gz subjb-to-subja_morph.nii.gz
>>>>>>>
>>>>>>> Thanks for your help,
>>>>>>>
>>>>>>> Vinny
>>>>>>>
>>>>>> -------------- next part --------------
>>>>>> An HTML attachment was scrubbed...
>>>>>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191118/e644a3c7/attachment-0001.html
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 18
>>>>>> Date: Mon, 18 Nov 2019 21:46:26 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <cbca25e6-d636-d10c-4224-096f49d5ebaa@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> why did you call it bert? It just makes things confusing
>>>>>>
>>>>>> On 11/18/19 2:53 PM, An wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Here is my recon-all command line:
>>>>>>> recon-all -i ana_Vol.nii -s bert -all
>>>>>>> Many thanks.
>>>>>>>
>>>>>>> Best,
>>>>>>> An
>>>>>>>
>>>>>>>
>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?18??? ??2:33???
>>>>>>>
>>>>>>>     What was your original recon-all command?
>>>>>>>
>>>>>>>     On 11/18/19 1:48 PM, An wrote:
>>>>>>>> ????????External Email - Use Caution
>>>>>>>>
>>>>>>>> I want to map the intensities of the volumes on its corresponding
>>>>>>>> surface in order to get the functional values on each vertex in
>>>>>>>     each
>>>>>>>> frame.?I ran recon-all for the anatomical volume and saved all
>>>>>>>> outputs(mri,labels,surf and etc.) in the bert folder. I use it
>>>>>>>     because
>>>>>>>> I need to specify?the required flag -s in bbregister in order to
>>>>>>>> register the functional volume to its anatomical volume.
>>>>>>>>
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>     ?2019?11?18??? ??1:31???
>>>>>>>> ? ? ?I don't understand what you are trying to do. I'm very
>>>>>>>     confused by
>>>>>>>> ? ? ?your
>>>>>>>> ? ? ?mentioning of bert. What does bert have to do with any of
>>>>>>>     your data?
>>>>>>>> ? ? ?On 11/14/19 10:47 AM, An wrote:
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Oops sorry for the mistakenly?reply. I will pay more attention
>>>>>>>> ? ? ?in the
>>>>>>>> ? ? ?> future.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Bert is the folder with the anatomical data. I tried the
>>>>>>>     following
>>>>>>>> ? ? ?> steps with the 4D volume but failed. Then I checked the
>>>>>>>> ? ? ?registration
>>>>>>>> ? ? ?> result after bbregister and found that the volume was not
>>>>>>>> ? ? ?registered.
>>>>>>>> ? ? ?> After that I tried another 4D volume to do the steps and
>>>>>>>> ? ? ?successfully
>>>>>>>> ? ? ?> got the sampled intensity onto the surface.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> The difference between the new 4D volume I used and the
>>>>>>>     previous
>>>>>>>> ? ? ?one
>>>>>>>> ? ? ?> is that there are two transformation matrices between
>>>>>>>     them. The 4D
>>>>>>>> ? ? ?> dataset that I previously used but failed is the volume
>>>>>>>     already
>>>>>>>> ? ? ?> registered to its anatomical volume(by using others
>>>>>>>     tools). The
>>>>>>>> ? ? ?new 4D
>>>>>>>> ? ? ?> volume that I tried and succeed is the volume not registered.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> I have no idea why the 4D volume after the transformation
>>>>>>>     would
>>>>>>>> ? ? ?cause
>>>>>>>> ? ? ?> a failed result. Could you please let me know that?
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Many thanks.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Best,
>>>>>>>> ? ? ?> An
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>>>>
>>>>>>>> ? ? ??2019?11?13??? ??12:20???
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>? ? ?If you have an anatomical MR that you have run through
>>>>>>>> ? ? ?recon-all,
>>>>>>>> ? ? ?>? ? ?then
>>>>>>>> ? ? ?>? ? ?just use that one instead of bert in your steps below
>>>>>>>> ? ? ?>? ? ?ps. Please remember to post to the FS list and not to us
>>>>>>>> ? ? ?personally
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>? ? ?On 11/12/19 8:41 PM, an wrote:
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Many thanks.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> I got the 4D fMRI dataset from others and it is not raw
>>>>>>>> ? ? ?data. In
>>>>>>>> ? ? ?>? ? ?order
>>>>>>>> ? ? ?>? ? ?> to run mri_vol2surf, I need to calculate the
>>>>>>>     register.dat
>>>>>>>> ? ? ?for the
>>>>>>>> ? ? ?>? ? ?> required flag --srcreg so I tried in this way.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> FYI, the 4D fMRI dataset should have been registered
>>>>>>>     with its
>>>>>>>> ? ? ?>? ? ?> anatomical MR volume by using other tools.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> For now I only ran the recon-all on its anatomical
>>>>>>>     MR volume
>>>>>>>> ? ? ?>? ? ?without
>>>>>>>> ? ? ?>? ? ?> running the functional stream as I don't have the
>>>>>>>     raw data.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Should I also run the raw fMRI data from scratch by
>>>>>>>     using
>>>>>>>> ? ? ?>? ? ?functional
>>>>>>>> ? ? ?>? ? ?> stream? Or if I can run mri_vol2surf independently,
>>>>>>>     which
>>>>>>>> ? ? ?command
>>>>>>>> ? ? ?>? ? ?> should I use to get a register.dat file?
>>>>>>>> ? ? ?>? ? ?> In addition, the intensity of the 4D fMRI dataset I have
>>>>>>>> ? ? ?is between
>>>>>>>> ? ? ?>? ? ?> [-1, 1] and not integers, would this cause any problem?
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Best,
>>>>>>>> ? ? ?>? ? ?> An
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>> ? ? ?>? ? ?>> Don't do the 1st step.
>>>>>>>> ? ? ?>? ? ?>> Why are you registering it to bert? I'm pretty sure
>>>>>>>     bert
>>>>>>>> ? ? ?did not
>>>>>>>> ? ? ?>? ? ?>> participate in your fmri study
>>>>>>>> ? ? ?>? ? ?>> When you run mri_vol2surf, it will probably work
>>>>>>>     better with
>>>>>>>> ? ? ?>? ? ?>> --projfrac 0.5
>>>>>>>> ? ? ?>? ? ?>>
>>>>>>>> ? ? ?>? ? ?>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> Hi Prof. Greve,
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> Thanks for your reply and sorry for the confusion.
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> I have a 4D fMRI dataset with 10 time frames,
>>>>>>>     where the
>>>>>>>> ? ? ?>? ? ?intensity of
>>>>>>>> ? ? ?>? ? ?>>> each voxel is between [-1,1] and not integers. I
>>>>>>>     want to
>>>>>>>> ? ? ?map the
>>>>>>>> ? ? ?>? ? ?>>> intensities of the volumes on its corresponding
>>>>>>>     surface in
>>>>>>>> ? ? ?>? ? ?order to
>>>>>>>> ? ? ?>? ? ?>>> get the functional values on each vertex in each
>>>>>>>     frame.
>>>>>>>> ? ? ?I have
>>>>>>>> ? ? ?>? ? ?>>> already run its corresponding anatomical image in
>>>>>>>> ? ? ?freesurfer.
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> To achieve it, I tried the following steps:
>>>>>>>> ? ? ?>? ? ?>>> 1. conform the fmri series by using mri_convert
>>>>>>>> ? ? ?>? ? ?>>> 2. register the fmri series with the anatomy image
>>>>>>>     by using
>>>>>>>> ? ? ?>? ? ?>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert
>>>>>>>     --reg
>>>>>>>> ? ? ?>? ? ?register.dat
>>>>>>>> ? ? ?>? ? ?>>> 3. assign values from volumes to each vertex by using
>>>>>>>> ? ? ?>? ? ?mri_vol2surf:
>>>>>>>> ? ? ?>? ? ?>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/
>>>>>>>     --srcreg
>>>>>>>> ? ? ?>? ? ?>>> register.dat --hemi lh
>>>>>>>> ? ? ?>? ? ?>>> ? ? I also tried the -regheader in mri_vol2surf:
>>>>>>>> ? ? ?mri_vol2surf
>>>>>>>> ? ? ?>? ? ?--src
>>>>>>>> ? ? ?>? ? ?>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert
>>>>>>>     --hemi lh
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>> ? ? ?>? ? ?freeview. But
>>>>>>>> ? ? ?>? ? ?>>> after step2, the registered volume looks wrong. I am
>>>>>>>> ? ? ?wondering
>>>>>>>> ? ? ?>? ? ?could
>>>>>>>> ? ? ?>? ? ?>>> I use bbregister to register multi-frame fMRI
>>>>>>>     series to
>>>>>>>> ? ? ?a single
>>>>>>>> ? ? ?>? ? ?>>> volume?
>>>>>>>> ? ? ?>? ? ?>>> I also tried to use --regheader to replace the
>>>>>>>     --srcreg
>>>>>>>> ? ? ?file in
>>>>>>>> ? ? ?>? ? ?>>> mri_vol2surf as the output register.dat in step2 is
>>>>>>>> ? ? ?wrong. But
>>>>>>>> ? ? ?>? ? ?the
>>>>>>>> ? ? ?>? ? ?>>> output is still wrong.
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> Many thanks.
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> Best,
>>>>>>>> ? ? ?>? ? ?>>> An
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>>>>> ?2019?11?11???
>>>>>>>> ? ? ???12:16???
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?When you say it is 4D, what do you mean? That
>>>>>>>     each label
>>>>>>>> ? ? ?>? ? ?has its
>>>>>>>> ? ? ?>? ? ?>>>? ? ?own frame?
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> Hi there,
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> I am working with creating a surface
>>>>>>>     parcellation
>>>>>>>> ? ? ?from a
>>>>>>>> ? ? ?>? ? ?>>>? ? ?volumetric
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> parcellation and have some questions as follows:
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> 1. If the volumetric parcellation is a
>>>>>>>     labeled 4D
>>>>>>>> ? ? ?>? ? ?multi-frame
>>>>>>>> ? ? ?>? ? ?>>>? ? ?dataset,
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> could I still use the mris_sample_parc? Or could
>>>>>>>> ? ? ?>? ? ?mri_vol2surf
>>>>>>>> ? ? ?>? ? ?>>>? ? ?get the
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> sampled labels for every vertex?
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> 2. For the 4D multi-frame dataset and
>>>>>>>     mri_vol2surf
>>>>>>>> ? ? ?output
>>>>>>>> ? ? ?>? ? ?>>>? ? ?results,
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> which GUI should I use to visualize it? I tried
>>>>>>>> ? ? ?freeview
>>>>>>>> ? ? ?>? ? ?for 4D
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> multi-frame dataset but it looks weird.
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> 3. Is there any command to separate?multi-frame
>>>>>>>> ? ? ?volume to
>>>>>>>> ? ? ?>? ? ?>>>? ? ?single frame
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> volumes?
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> Many thanks!
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> Best,
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> An
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> _______________________________________________
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> ?_______________________________________________
>>>>>>>> ? ? ?>? ? ?>>>? ? ?Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> _______________________________________________
>>>>>>>> ? ? ?>? ? ?>>> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>>
>>>>>>>> ? ? ?>? ? ?>>
>>>>>>>> ? ? ?>? ? ?>> _______________________________________________
>>>>>>>> ? ? ?>? ? ?>> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>>
>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>? ? ?The information in this e-mail is intended only for the
>>>>>>>> ? ? ?person to
>>>>>>>> ? ? ?>? ? ?whom it is
>>>>>>>> ? ? ?>? ? ?addressed. If you believe this e-mail was sent to you in
>>>>>>>> ? ? ?error and
>>>>>>>> ? ? ?>? ? ?the e-mail
>>>>>>>> ? ? ?>? ? ?contains patient information, please contact the Partners
>>>>>>>> ? ? ?>? ? ?Compliance HelpLine at
>>>>>>>> ? ? ?> http://www.partners.org/complianceline . If the e-mail was
>>>>>>>     sent to
>>>>>>>> ? ? ?>? ? ?you in error
>>>>>>>> ? ? ?>? ? ?but does not contain patient information, please
>>>>>>>     contact the
>>>>>>>> ? ? ?>? ? ?sender and properly
>>>>>>>> ? ? ?>? ? ?dispose of the e-mail.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> _______________________________________________
>>>>>>>> ? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
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>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> ? ? ?_______________________________________________
>>>>>>>> ? ? ?Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>     _______________________________________________
>>>>>>>     Freesurfer mailing list
>>>>>>>     Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 19
>>>>>> Date: Mon, 18 Nov 2019 17:04:32 -0500
>>>>>> From: An <annaqu1024@gmail.com>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <CAJVCUNeKHVUw-22tnVxwUDR6pXh=1_qMuqsiL1qONJTZRSP1kQ@mail.gmail.com>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>         External Email - Use Caution
>>>>>>
>>>>>> Sorry for the confusion, I don't know it has a delicated meaning. I just
>>>>>> followed the steps on the freesurfer download and install webpage to
>>>>>> install the software and then ran the recon-all command.  I will try to
>>>>>> avoid this kind of issues in the future.
>>>>>>
>>>>>> Many thanks.
>>>>>>
>>>>>> Best,
>>>>>> An
>>>>>>
>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> ?2019?11?18??? ??4:47???
>>>>>>
>>>>>>> why did you call it bert? It just makes things confusing
>>>>>>>
>>>>>>> On 11/18/19 2:53 PM, An wrote:
>>>>>>>>         External Email - Use Caution
>>>>>>>>
>>>>>>>> Here is my recon-all command line:
>>>>>>>> recon-all -i ana_Vol.nii -s bert -all
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>>
>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?18??? ??2:33???
>>>>>>>>
>>>>>>>>     What was your original recon-all command?
>>>>>>>>
>>>>>>>>     On 11/18/19 1:48 PM, An wrote:
>>>>>>>>>         External Email - Use Caution
>>>>>>>>>
>>>>>>>>> I want to map the intensities of the volumes on its corresponding
>>>>>>>>> surface in order to get the functional values on each vertex in
>>>>>>>>     each
>>>>>>>>> frame. I ran recon-all for the anatomical volume and saved all
>>>>>>>>> outputs(mri,labels,surf and etc.) in the bert folder. I use it
>>>>>>>>     because
>>>>>>>>> I need to specify the required flag -s in bbregister in order to
>>>>>>>>> register the functional volume to its anatomical volume.
>>>>>>>>>
>>>>>>>>> Many thanks.
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> An
>>>>>>>>>
>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>>     ?2019?11?18??? ??1:31???
>>>>>>>>>     I don't understand what you are trying to do. I'm very
>>>>>>>>     confused by
>>>>>>>>>     your
>>>>>>>>>     mentioning of bert. What does bert have to do with any of
>>>>>>>>     your data?
>>>>>>>>>     On 11/14/19 10:47 AM, An wrote:
>>>>>>>>>>         External Email - Use Caution
>>>>>>>>>>
>>>>>>>>>> Oops sorry for the mistakenly reply. I will pay more
>>>>>>> attention
>>>>>>>>>     in the
>>>>>>>>>> future.
>>>>>>>>>>
>>>>>>>>>> Bert is the folder with the anatomical data. I tried the
>>>>>>>>     following
>>>>>>>>>> steps with the 4D volume but failed. Then I checked the
>>>>>>>>>     registration
>>>>>>>>>> result after bbregister and found that the volume was not
>>>>>>>>>     registered.
>>>>>>>>>> After that I tried another 4D volume to do the steps and
>>>>>>>>>     successfully
>>>>>>>>>> got the sampled intensity onto the surface.
>>>>>>>>>>
>>>>>>>>>> The difference between the new 4D volume I used and the
>>>>>>>>     previous
>>>>>>>>>     one
>>>>>>>>>> is that there are two transformation matrices between
>>>>>>>>     them. The 4D
>>>>>>>>>> dataset that I previously used but failed is the volume
>>>>>>>>     already
>>>>>>>>>> registered to its anatomical volume(by using others
>>>>>>>>     tools). The
>>>>>>>>>     new 4D
>>>>>>>>>> volume that I tried and succeed is the volume not registered.
>>>>>>>>>>
>>>>>>>>>> I have no idea why the 4D volume after the transformation
>>>>>>>>     would
>>>>>>>>>     cause
>>>>>>>>>> a failed result. Could you please let me know that?
>>>>>>>>>>
>>>>>>>>>> Many thanks.
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>> An
>>>>>>>>>>
>>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>>
>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>>>>
>>>>>>>>>     ?2019?11?13??? ??12:20???
>>>>>>>>>>     If you have an anatomical MR that you have run through
>>>>>>>>>     recon-all,
>>>>>>>>>>     then
>>>>>>>>>>     just use that one instead of bert in your steps below
>>>>>>>>>>     ps. Please remember to post to the FS list and not to us
>>>>>>>>>     personally
>>>>>>>>>>     On 11/12/19 8:41 PM, an wrote:
>>>>>>>>>>>         External Email - Use Caution
>>>>>>>>>>>
>>>>>>>>>>> Many thanks.
>>>>>>>>>>>
>>>>>>>>>>> I got the 4D fMRI dataset from others and it is not raw
>>>>>>>>>     data. In
>>>>>>>>>>     order
>>>>>>>>>>> to run mri_vol2surf, I need to calculate the
>>>>>>>>     register.dat
>>>>>>>>>     for the
>>>>>>>>>>> required flag --srcreg so I tried in this way.
>>>>>>>>>>>
>>>>>>>>>>> FYI, the 4D fMRI dataset should have been registered
>>>>>>>>     with its
>>>>>>>>>>> anatomical MR volume by using other tools.
>>>>>>>>>>>
>>>>>>>>>>> For now I only ran the recon-all on its anatomical
>>>>>>>>     MR volume
>>>>>>>>>>     without
>>>>>>>>>>> running the functional stream as I don't have the
>>>>>>>>     raw data.
>>>>>>>>>>> Should I also run the raw fMRI data from scratch by
>>>>>>>>     using
>>>>>>>>>>     functional
>>>>>>>>>>> stream? Or if I can run mri_vol2surf independently,
>>>>>>>>     which
>>>>>>>>>     command
>>>>>>>>>>> should I use to get a register.dat file?
>>>>>>>>>>> In addition, the intensity of the 4D fMRI dataset I
>>>>>>> have
>>>>>>>>>     is between
>>>>>>>>>>> [-1, 1] and not integers, would this cause any problem?
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>> An
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>>>>>> Don't do the 1st step.
>>>>>>>>>>>> Why are you registering it to bert? I'm pretty sure
>>>>>>>>     bert
>>>>>>>>>     did not
>>>>>>>>>>>> participate in your fmri study
>>>>>>>>>>>> When you run mri_vol2surf, it will probably work
>>>>>>>>     better with
>>>>>>>>>>>> --projfrac 0.5
>>>>>>>>>>>>
>>>>>>>>>>>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>>>>>>>         External Email - Use Caution
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Prof. Greve,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks for your reply and sorry for the confusion.
>>>>>>>>>>>>>
>>>>>>>>>>>>> I have a 4D fMRI dataset with 10 time frames,
>>>>>>>>     where the
>>>>>>>>>>     intensity of
>>>>>>>>>>>>> each voxel is between [-1,1] and not integers. I
>>>>>>>>     want to
>>>>>>>>>     map the
>>>>>>>>>>>>> intensities of the volumes on its corresponding
>>>>>>>>     surface in
>>>>>>>>>>     order to
>>>>>>>>>>>>> get the functional values on each vertex in each
>>>>>>>>     frame.
>>>>>>>>>     I have
>>>>>>>>>>>>> already run its corresponding anatomical image in
>>>>>>>>>     freesurfer.
>>>>>>>>>>>>> To achieve it, I tried the following steps:
>>>>>>>>>>>>> 1. conform the fmri series by using mri_convert
>>>>>>>>>>>>> 2. register the fmri series with the anatomy image
>>>>>>>>     by using
>>>>>>>>>>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert
>>>>>>>>     --reg
>>>>>>>>>>     register.dat
>>>>>>>>>>>>> 3. assign values from volumes to each vertex by using
>>>>>>>>>>     mri_vol2surf:
>>>>>>>>>>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/
>>>>>>>>     --srcreg
>>>>>>>>>>>>> register.dat --hemi lh
>>>>>>>>>>>>>     I also tried the -regheader in mri_vol2surf:
>>>>>>>>>     mri_vol2surf
>>>>>>>>>>     --src
>>>>>>>>>>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert
>>>>>>>>     --hemi lh
>>>>>>>>>>>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>>>>     freeview. But
>>>>>>>>>>>>> after step2, the registered volume looks wrong. I am
>>>>>>>>>     wondering
>>>>>>>>>>     could
>>>>>>>>>>>>> I use bbregister to register multi-frame fMRI
>>>>>>>>     series to
>>>>>>>>>     a single
>>>>>>>>>>>>> volume?
>>>>>>>>>>>>> I also tried to use --regheader to replace the
>>>>>>>>     --srcreg
>>>>>>>>>     file in
>>>>>>>>>>>>> mri_vol2surf as the output register.dat in step2 is
>>>>>>>>>     wrong. But
>>>>>>>>>>     the
>>>>>>>>>>>>> output is still wrong.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Many thanks.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Best,
>>>>>>>>>>>>> An
>>>>>>>>>>>>>
>>>>>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>>
>>>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>>
>>>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>     <mailto:DGREVE@mgh.harvard.edu>>>>> ?2019?11?11???
>>>>>>>>>     ??12:16???
>>>>>>>>>>>>>     When you say it is 4D, what do you mean? That
>>>>>>>>     each label
>>>>>>>>>>     has its
>>>>>>>>>>>>>     own frame?
>>>>>>>>>>>>>
>>>>>>>>>>>>>     On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>>>>>>>>         External Email - Use Caution
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi there,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I am working with creating a surface
>>>>>>>>     parcellation
>>>>>>>>>     from a
>>>>>>>>>>>>>     volumetric
>>>>>>>>>>>>>> parcellation and have some questions as
>>>>>>> follows:
>>>>>>>>>>>>>> 1. If the volumetric parcellation is a
>>>>>>>>     labeled 4D
>>>>>>>>>>     multi-frame
>>>>>>>>>>>>>     dataset,
>>>>>>>>>>>>>> could I still use the mris_sample_parc? Or
>>>>>>> could
>>>>>>>>>>     mri_vol2surf
>>>>>>>>>>>>>     get the
>>>>>>>>>>>>>> sampled labels for every vertex?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 2. For the 4D multi-frame dataset and
>>>>>>>>     mri_vol2surf
>>>>>>>>>     output
>>>>>>>>>>>>>     results,
>>>>>>>>>>>>>> which GUI should I use to visualize it? I tried
>>>>>>>>>     freeview
>>>>>>>>>>     for 4D
>>>>>>>>>>>>>> multi-frame dataset but it looks weird.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 3. Is there any command to separate multi-frame
>>>>>>>>>     volume to
>>>>>>>>>>>>>     single frame
>>>>>>>>>>>>>> volumes?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Many thanks!
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>> An
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>     Freesurfer mailing list
>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>     The information in this e-mail is intended only for the
>>>>>>>>>     person to
>>>>>>>>>>     whom it is
>>>>>>>>>>     addressed. If you believe this e-mail was sent to you in
>>>>>>>>>     error and
>>>>>>>>>>     the e-mail
>>>>>>>>>>     contains patient information, please contact the Partners
>>>>>>>>>>     Compliance HelpLine at
>>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was
>>>>>>>>     sent to
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>>>>>>>>>>     but does not contain patient information, please
>>>>>>>>     contact the
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
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>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>     _______________________________________________
>>>>>>>>>     Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>     _______________________________________________
>>>>>>>>     Freesurfer mailing list
>>>>>>>>     Freesurfer@nmr.mgh.harvard.edu <mailto:
>>>>>>> Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
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>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> -------------- next part --------------
>>>>>> An HTML attachment was scrubbed...
>>>>>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191118/d835731d/attachment-0001.html
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 20
>>>>>> Date: Mon, 18 Nov 2019 17:14:27 -0500 (EST)
>>>>>> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <alpine.LRH.2.20.1911181714130.28427@gate.nmr.mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> it's not delicate - it's just confusing for us when you use it as it
>>>>>> refers to a specific dataset
>>>>>>
>>>>>> cheers
>>>>>> Bruce
>>>>>> On Mon, 18 Nov 2019, An wrote:
>>>>>>
>>>>>>> ????????External Email - Use Caution????????
>>>>>>>
>>>>>>> Sorry for the confusion, I don't know it has a delicated meaning. I just followed the steps on the
>>>>>>> freesurfer download and install webpage to install the software and then ran the recon-all command.?
>>>>>>> I will try to avoid this kind of issues in the future.
>>>>>>> Many thanks.
>>>>>>>
>>>>>>> Best,
>>>>>>> An
>>>>>>>
>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> ?2019?11?18??? ??4:47???
>>>>>>>       why did you call it bert? It just makes things confusing
>>>>>>>
>>>>>>>       On 11/18/19 2:53 PM, An wrote:
>>>>>>>> ????????External Email - Use Caution
>>>>>>>>
>>>>>>>> Here is my recon-all command line:
>>>>>>>> recon-all -i ana_Vol.nii -s bert -all
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>>
>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?18??? ??2:33???
>>>>>>>>
>>>>>>>> ? ? ?What was your original recon-all command?
>>>>>>>>
>>>>>>>> ? ? ?On 11/18/19 1:48 PM, An wrote:
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> I want to map the intensities of the volumes on its corresponding
>>>>>>>> ? ? ?> surface in order to get the functional values on each vertex in
>>>>>>>> ? ? ?each
>>>>>>>> ? ? ?> frame.?I ran recon-all for the anatomical volume and saved all
>>>>>>>> ? ? ?> outputs(mri,labels,surf and etc.) in the bert folder. I use it
>>>>>>>> ? ? ?because
>>>>>>>> ? ? ?> I need to specify?the required flag -s in bbregister in order to
>>>>>>>> ? ? ?> register the functional volume to its anatomical volume.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Many thanks.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Best,
>>>>>>>> ? ? ?> An
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>> ? ? ??2019?11?18??? ??1:31???
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>? ? ?I don't understand what you are trying to do. I'm very
>>>>>>>> ? ? ?confused by
>>>>>>>> ? ? ?>? ? ?your
>>>>>>>> ? ? ?>? ? ?mentioning of bert. What does bert have to do with any of
>>>>>>>> ? ? ?your data?
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>? ? ?On 11/14/19 10:47 AM, An wrote:
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Oops sorry for the mistakenly?reply. I will pay more attention
>>>>>>>> ? ? ?>? ? ?in the
>>>>>>>> ? ? ?>? ? ?> future.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Bert is the folder with the anatomical data. I tried the
>>>>>>>> ? ? ?following
>>>>>>>> ? ? ?>? ? ?> steps with the 4D volume but failed. Then I checked the
>>>>>>>> ? ? ?>? ? ?registration
>>>>>>>> ? ? ?>? ? ?> result after bbregister and found that the volume was not
>>>>>>>> ? ? ?>? ? ?registered.
>>>>>>>> ? ? ?>? ? ?> After that I tried another 4D volume to do the steps and
>>>>>>>> ? ? ?>? ? ?successfully
>>>>>>>> ? ? ?>? ? ?> got the sampled intensity onto the surface.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> The difference between the new 4D volume I used and the
>>>>>>>> ? ? ?previous
>>>>>>>> ? ? ?>? ? ?one
>>>>>>>> ? ? ?>? ? ?> is that there are two transformation matrices between
>>>>>>>> ? ? ?them. The 4D
>>>>>>>> ? ? ?>? ? ?> dataset that I previously used but failed is the volume
>>>>>>>> ? ? ?already
>>>>>>>> ? ? ?>? ? ?> registered to its anatomical volume(by using others
>>>>>>>> ? ? ?tools). The
>>>>>>>> ? ? ?>? ? ?new 4D
>>>>>>>> ? ? ?>? ? ?> volume that I tried and succeed is the volume not registered.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> I have no idea why the 4D volume after the transformation
>>>>>>>> ? ? ?would
>>>>>>>> ? ? ?>? ? ?cause
>>>>>>>> ? ? ?>? ? ?> a failed result. Could you please let me know that?
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Many thanks.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Best,
>>>>>>>> ? ? ?>? ? ?> An
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>>>>
>>>>>>>> ? ? ?>? ? ??2019?11?13??? ??12:20???
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?If you have an anatomical MR that you have run through
>>>>>>>> ? ? ?>? ? ?recon-all,
>>>>>>>> ? ? ?>? ? ?>? ? ?then
>>>>>>>> ? ? ?>? ? ?>? ? ?just use that one instead of bert in your steps below
>>>>>>>> ? ? ?>? ? ?>? ? ?ps. Please remember to post to the FS list and not to us
>>>>>>>> ? ? ?>? ? ?personally
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?On 11/12/19 8:41 PM, an wrote:
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> Many thanks.
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> I got the 4D fMRI dataset from others and it is not raw
>>>>>>>> ? ? ?>? ? ?data. In
>>>>>>>> ? ? ?>? ? ?>? ? ?order
>>>>>>>> ? ? ?>? ? ?>? ? ?> to run mri_vol2surf, I need to calculate the
>>>>>>>> ? ? ?register.dat
>>>>>>>> ? ? ?>? ? ?for the
>>>>>>>> ? ? ?>? ? ?>? ? ?> required flag --srcreg so I tried in this way.
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> FYI, the 4D fMRI dataset should have been registered
>>>>>>>> ? ? ?with its
>>>>>>>> ? ? ?>? ? ?>? ? ?> anatomical MR volume by using other tools.
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> For now I only ran the recon-all on its anatomical
>>>>>>>> ? ? ?MR volume
>>>>>>>> ? ? ?>? ? ?>? ? ?without
>>>>>>>> ? ? ?>? ? ?>? ? ?> running the functional stream as I don't have the
>>>>>>>> ? ? ?raw data.
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> Should I also run the raw fMRI data from scratch by
>>>>>>>> ? ? ?using
>>>>>>>> ? ? ?>? ? ?>? ? ?functional
>>>>>>>> ? ? ?>? ? ?>? ? ?> stream? Or if I can run mri_vol2surf independently,
>>>>>>>> ? ? ?which
>>>>>>>> ? ? ?>? ? ?command
>>>>>>>> ? ? ?>? ? ?>? ? ?> should I use to get a register.dat file?
>>>>>>>> ? ? ?>? ? ?>? ? ?> In addition, the intensity of the 4D fMRI dataset I have
>>>>>>>> ? ? ?>? ? ?is between
>>>>>>>> ? ? ?>? ? ?>? ? ?> [-1, 1] and not integers, would this cause any problem?
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> Best,
>>>>>>>> ? ? ?>? ? ?>? ? ?> An
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>> ? ? ?>? ? ?>? ? ?>> Don't do the 1st step.
>>>>>>>> ? ? ?>? ? ?>? ? ?>> Why are you registering it to bert? I'm pretty sure
>>>>>>>> ? ? ?bert
>>>>>>>> ? ? ?>? ? ?did not
>>>>>>>> ? ? ?>? ? ?>? ? ?>> participate in your fmri study
>>>>>>>> ? ? ?>? ? ?>? ? ?>> When you run mri_vol2surf, it will probably work
>>>>>>>> ? ? ?better with
>>>>>>>> ? ? ?>? ? ?>? ? ?>> --projfrac 0.5
>>>>>>>> ? ? ?>? ? ?>? ? ?>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Hi Prof. Greve,
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Thanks for your reply and sorry for the confusion.
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> I have a 4D fMRI dataset with 10 time frames,
>>>>>>>> ? ? ?where the
>>>>>>>> ? ? ?>? ? ?>? ? ?intensity of
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> each voxel is between [-1,1] and not integers. I
>>>>>>>> ? ? ?want to
>>>>>>>> ? ? ?>? ? ?map the
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> intensities of the volumes on its corresponding
>>>>>>>> ? ? ?surface in
>>>>>>>> ? ? ?>? ? ?>? ? ?order to
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> get the functional values on each vertex in each
>>>>>>>> ? ? ?frame.
>>>>>>>> ? ? ?>? ? ?I have
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> already run its corresponding anatomical image in
>>>>>>>> ? ? ?>? ? ?freesurfer.
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> To achieve it, I tried the following steps:
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> 1. conform the fmri series by using mri_convert
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> 2. register the fmri series with the anatomy image
>>>>>>>> ? ? ?by using
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert
>>>>>>>> ? ? ?--reg
>>>>>>>> ? ? ?>? ? ?>? ? ?register.dat
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> 3. assign values from volumes to each vertex by using
>>>>>>>> ? ? ?>? ? ?>? ? ?mri_vol2surf:
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/
>>>>>>>> ? ? ?--srcreg
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> register.dat --hemi lh
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> ? ? I also tried the -regheader in mri_vol2surf:
>>>>>>>> ? ? ?>? ? ?mri_vol2surf
>>>>>>>> ? ? ?>? ? ?>? ? ?--src
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert
>>>>>>>> ? ? ?--hemi lh
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>> ? ? ?>? ? ?>? ? ?freeview. But
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> after step2, the registered volume looks wrong. I am
>>>>>>>> ? ? ?>? ? ?wondering
>>>>>>>> ? ? ?>? ? ?>? ? ?could
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> I use bbregister to register multi-frame fMRI
>>>>>>>> ? ? ?series to
>>>>>>>> ? ? ?>? ? ?a single
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> volume?
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> I also tried to use --regheader to replace the
>>>>>>>> ? ? ?--srcreg
>>>>>>>> ? ? ?>? ? ?file in
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> mri_vol2surf as the output register.dat in step2 is
>>>>>>>> ? ? ?>? ? ?wrong. But
>>>>>>>> ? ? ?>? ? ?>? ? ?the
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> output is still wrong.
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Many thanks.
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Best,
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> An
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>>>>> ?2019?11?11???
>>>>>>>> ? ? ?>? ? ???12:16???
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?When you say it is 4D, what do you mean? That
>>>>>>>> ? ? ?each label
>>>>>>>> ? ? ?>? ? ?>? ? ?has its
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?own frame?
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> Hi there,
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> I am working with creating a surface
>>>>>>>> ? ? ?parcellation
>>>>>>>> ? ? ?>? ? ?from a
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?volumetric
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> parcellation and have some questions as follows:
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> 1. If the volumetric parcellation is a
>>>>>>>> ? ? ?labeled 4D
>>>>>>>> ? ? ?>? ? ?>? ? ?multi-frame
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?dataset,
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> could I still use the mris_sample_parc? Or could
>>>>>>>> ? ? ?>? ? ?>? ? ?mri_vol2surf
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?get the
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> sampled labels for every vertex?
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> 2. For the 4D multi-frame dataset and
>>>>>>>> ? ? ?mri_vol2surf
>>>>>>>> ? ? ?>? ? ?output
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?results,
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> which GUI should I use to visualize it? I tried
>>>>>>>> ? ? ?>? ? ?freeview
>>>>>>>> ? ? ?>? ? ?>? ? ?for 4D
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> multi-frame dataset but it looks weird.
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> 3. Is there any command to separate?multi-frame
>>>>>>>> ? ? ?>? ? ?volume to
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?single frame
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> volumes?
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> Many thanks!
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> Best,
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> An
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> _______________________________________________
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> ?_______________________________________________
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> _______________________________________________
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>? ? ?>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>> _______________________________________________
>>>>>>>> ? ? ?>? ? ?>? ? ?>> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>? ? ?>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>
>>>>>>>> ? ? ?https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?The information in this e-mail is intended only for the
>>>>>>>> ? ? ?>? ? ?person to
>>>>>>>> ? ? ?>? ? ?>? ? ?whom it is
>>>>>>>> ? ? ?>? ? ?>? ? ?addressed. If you believe this e-mail was sent to you in
>>>>>>>> ? ? ?>? ? ?error and
>>>>>>>> ? ? ?>? ? ?>? ? ?the e-mail
>>>>>>>> ? ? ?>? ? ?>? ? ?contains patient information, please contact the Partners
>>>>>>>> ? ? ?>? ? ?>? ? ?Compliance HelpLine at
>>>>>>>> ? ? ?>? ? ?> http://www.partners.org/complianceline . If the e-mail was
>>>>>>>> ? ? ?sent to
>>>>>>>> ? ? ?>? ? ?>? ? ?you in error
>>>>>>>> ? ? ?>? ? ?>? ? ?but does not contain patient information, please
>>>>>>>> ? ? ?contact the
>>>>>>>> ? ? ?>? ? ?>? ? ?sender and properly
>>>>>>>> ? ? ?>? ? ?>? ? ?dispose of the e-mail.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> _______________________________________________
>>>>>>>> ? ? ?>? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>? ? ?_______________________________________________
>>>>>>>> ? ? ?>? ? ?Freesurfer mailing list
>>>>>>>> ? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> _______________________________________________
>>>>>>>> ? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> ? ? ?_______________________________________________
>>>>>>>> ? ? ?Freesurfer mailing list
>>>>>>>> ? ? ?Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>       _______________________________________________
>>>>>>>       Freesurfer mailing list
>>>>>>>       Freesurfer@nmr.mgh.harvard.edu
>>>>>>>       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 21
>>>>>> Date: Tue, 19 Nov 2019 01:59:48 +0000
>>>>>> From: An Lijun <lijun.an@hotmail.com>
>>>>>> Subject: Re: [Freesurfer] Volume (WM Parcellation) of
>>>>>>   RightCerebralCortex--Freesurfer 6.0
>>>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <CWXP123MB2182C7D7E2C53FD2999CD0149A4C0@CWXP123MB2182.GBRP123.PROD.OUTLOOK.COM>
>>>>>>  
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>         External Email - Use Caution
>>>>>>
>>>>>> Thanks for your reply!
>>>>>> You mean LeftCerebralCortex is actually lhCortex in aseg.stats, right?
>>>>>>
>>>>>> Best Regards,
>>>>>> An Lijun
>>>>>>
>>>>>>
>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> ?2019?11?19??? ??2:20???
>>>>>> You can find it in aseg.stats under
>>>>>>
>>>>>> # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter
>>>>>> volume, 272816.537999, mm^3
>>>>>> # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter
>>>>>> volume, 260016.082731, mm^3
>>>>>> # Measure Cortex, CortexVol, Total cortical gray matter volume,
>>>>>> 532832.620730, mm^3
>>>>>>
>>>>>>
>>>>>> On 11/13/19 11:54 PM, An Lijun wrote:
>>>>>>>         External Email - Use Caution
>>>>>>>
>>>>>>> Dear Freesurfer experts,
>>>>>>>
>>>>>>> I am trying to use ADNI MERGE R package to get 'wholebrain' volume.
>>>>>>>
>>>>>>> It requires <Left/Right>CerebralCortex. The information I get from
>>>>>>> ADNI merge is "*Volume (WM Parcellation) of RightCerebralCortex*".
>>>>>>>
>>>>>>> But when I ran Freesurfer reconall 6.0, I could not
>>>>>>> find <Left/Right>CerebralCortex under 'stats' folder, do you know
>>>>>>> where it could be? Thanks so much.
>>>>>>>
>>>>>>> Best Regards,
>>>>>>> An Lijun
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> -------------- next part --------------
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>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 22
>>>>>> Date: Tue, 19 Nov 2019 10:13:03 +0100
>>>>>> From: fsbuild <fsbuild@contbay.com>
>>>>>> Subject: Re: [Freesurfer] Custom location of license file
>>>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>>>> Cc: khs3z@virginia.edu
>>>>>> Message-ID: <1574154783.5dd3b21f76929@trashmail.com>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>         External Email - Use Caution
>>>>>>
>>>>>> Hello Karsten,
>>>>>>
>>>>>>
>>>>>>
>>>>>> Another option would be to try the 6.0.1 freesurfer release,
>>>>>>
>>>>>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz
>>>>>>
>>>>>>
>>>>>>
>>>>>> I've been told that it works in this release to set the FS_LICENSE environment variable to the path of license.txt
>>>>>>
>>>>>>
>>>>>>
>>>>>> - R.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>           fsbuild        November 15, 2019 at 03:25
>>>>>>   &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello Karsten,
>>>>>> I
>>>>>> think the location for license.txt in the freesurfer 6 release needs to
>>>>>> be under $FREESURFER_HOME, ie., $FREESURFER_HOME/license.txt, and
>>>>>> cannot be relocated from there by an environment variable. &nbsp;But you can
>>>>>> try using a soft link to point to it in another location. &nbsp;
>>>>>> While
>>>>>> it does not work to preserve $HOME/license.txt as a reference in
>>>>>> another environment variable like FREESURFER_HOME or within a soft link,
>>>>>> I believe the shorthand notation ~/license.txt does work in a soft
>>>>>> link. &nbsp; So in your common installation under $FREESURFER_HOME you could
>>>>>> try,
>>>>>> $ cd $FREESURFER_HOME$ ln -s ~/license.txt license.txt
>>>>>> - and see if freesurfer complains if an individual users $HOME/license.txt (or ~/license.txt) is missing.
>>>>>> In
>>>>>> the newer code base on the freesurfer development branch, it should
>>>>>> work to set the FS_LICENSE environment variable to point to the path of
>>>>>> the license.txt file, but I don?t think that works in the 6.0.0 release.
>>>>>> Ideally,
>>>>>> I think the freesurfer group would prefer if each user signed up for
>>>>>> their own license in order to track usage, so maybe try the soft link.
>>>>>>
>>>>>> - R.
>>>>>>
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> -------------- next part --------------
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>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 23
>>>>>> Date: Tue, 19 Nov 2019 10:00:10 +0000
>>>>>> From: "Ferraro, Pilar" <FerraroP@pennmedicine.upenn.edu>
>>>>>> Subject: [Freesurfer] Fwd: surface group analysis with qdec
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <EFCBCEB2-43EF-4B98-9D62-E56C3960D041@pennmedicine.upenn.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>         External Email - Use Caution
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I?ve never got a response to my last email (you can find it below).
>>>>>>
>>>>>> Would you be able to let me know so I can proceed with the analyses?
>>>>>>
>>>>>> Many thanks,
>>>>>>
>>>>>> Pilar
>>>>>>
>>>>>> Inizio messaggio inoltrato:
>>>>>>
>>>>>> Da: "Ferraro, Pilar" <FerraroP@pennmedicine.upenn.edu<mailto:FerraroP@pennmedicine.upenn.edu>>
>>>>>> Oggetto: Fw: surface group analysis with qdec
>>>>>> Data: 14 novembre 2019 3:47:42 PM CET
>>>>>> A: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I'm trying to run a surface based group analysis comparing patients and HC, correcting for disease duration.
>>>>>> I enclose here the fsgd file and the design matrix.
>>>>>> I've followed all the steps of the tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0) with no errors.
>>>>>> However, when I try to run the glm analysis with the following command:
>>>>>>
>>>>>> mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.dur.glmdir
>>>>>>
>>>>>> I get the error:
>>>>>>
>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>>>>>> --------------------------------
>>>>>> Possible problem with experimental design:
>>>>>> Check for duplicate entries and/or lack of range of
>>>>>> continuous variables within a class.
>>>>>>
>>>>>> Of course there is no range for the continuous variable (disease duration) in the control group, so I'm wondering how to overcome this limit and proceed correctly with the glm analysis.
>>>>>>
>>>>>> Many thanks in advance for any help you will provide,
>>>>>>
>>>>>> Pilar
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ________________________________
>>>>>> From: Ferraro, Pilar
>>>>>> Sent: Monday, November 11, 2019 7:07 AM
>>>>>> To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>>>> Subject: surface group analysis with qdec
>>>>>>
>>>>>> Hi!
>>>>>>
>>>>>> I've previously run a comparison between patients and HC using qdec, but now I'd like to correct the analysis for disease duration.
>>>>>> I've therefore generated a second qdec.table.dat file inserting the disease duration column with the following structure:
>>>>>> fsid group duration
>>>>>> Input subj1 1 13
>>>>>> Input subj2 0
>>>>>>
>>>>>> (For healthy controls group (group 0) I've tried both options, leaving the duration column blank or inserting 0 as a value).
>>>>>> I've also left the group.level file the same of the previous analysis.
>>>>>> However, when i open the new qdec.table.dat file with qdec I get problems in correctly uploading the data.
>>>>>> In particular, I get the following error:
>>>>>>
>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>>>>>> Possible problem with experimental design:
>>>>>> Check for duplicate entries and/or lack of range of continuous variables within a class.
>>>>>> If you seek help with this problem, make sure to send:
>>>>>> This is the command line:
>>>>>> mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh --fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods --glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage lh --label /home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat
>>>>>>
>>>>>> Of course there is no range for the continuous variable (disease duration) in the control group, so I'm wondering how to overcome this and generate a correct qdec.table.dat file.
>>>>>>
>>>>>> Thanks in advance for any help!
>>>>>>
>>>>>> Pilar
>>>>>>
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>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> End of Freesurfer Digest, Vol 189, Issue 26
>>>>>> *******************************************
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 9
>>>> Date: Wed, 20 Nov 2019 23:02:18 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] Freesurfer analyses in MATLAB
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <327663f6-966a-6f5a-71d5-f53adcb3b7a3@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> sorry, I don't know what it is you are doing here. what are beta2 and
>>>> X2? what is DV? what are you plotting against what?
>>>>
>>>> On 11/14/19 3:25 PM, cody samth wrote:
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> Hi I'm interested in running some analyses in matlab using freesurfer
>>>>> commands. I'm running an interaction effect, however I'm having issues
>>>>> residualizing the brain values to plot.
>>>>>
>>>>> For running interaction effects I'm running it by inputting:
>>>>>
>>>>> X=load('Xg.dat')
>>>>> Y=load('ROI.dat')
>>>>> C=load('C.dat')
>>>>> [beta rvar]=fast_glmfit(y,x)
>>>>> [F pvalues]=fast_fratio(beta,X.rvar.C)
>>>>>
>>>>> Which works correctly, then to residualize the values to plot against
>>>>> my DV I was inputting:
>>>>>
>>>>> X=load('Xg.dat')
>>>>> Y=load('ROI.dat')
>>>>> beta=inv(X'*X)*(X'*Y)
>>>>> beta2=load('beta.txt) ; nuisance beta coefficients removed
>>>>> X2=load('X2.dat') ; nuisance columns removed
>>>>> yhat=X2*beta2
>>>>>
>>>>> However the issue I'm having is when plotting the yhat against my
>>>>> variable of interest is that yhat is perfectly?predicted by my DV.
>>>>> This is the case for any ROI I test which makes me suspect i have an
>>>>> error in the matrix somewhere. I've attached a graph and can send the
>>>>> .dat files if needed.
>>>>> Screen Shot 2019-11-14 at 3.08.37 PM.png
>>>>>
>>>>> Thanks,
>>>>> Cody
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 10
>>>> Date: Thu, 21 Nov 2019 07:14:01 +0100
>>>> From: fsbuild <fsbuild@contbay.com>
>>>> Subject: Re: [Freesurfer] Freesurfer 4.5 on Ubuntu 18.04 ?
>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>> Cc: paulo_baptista@brown.edu
>>>> Message-ID: <1574316841.5dd62b29c075d@trashmail.com>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>>         External Email - Use Caution
>>>>
>>>> Hello Paulo,
>>>> What is the location of the freesurfer license file (?), i.e., I would make sure the freesurfer license file is under $FREESURFER_HOME and then see if you get different results running the command.
>>>> Even with the license file though, I?m not sure all the Freesurfer 4 binaries will run on Ubuntu 18
>>>> - R.
>>>> On Nov 19, 2019, at 15:26, Baptista, Paulo &lt;paulo_baptista@brown.edu&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello FreeSurfer Developers,I am helping a researcher in my department run FreeSurfer on a new computer.&nbsp; They insist that it should run on FreeSurfer 4.5 because their old system ran that version.&nbsp; Is the following possible?&nbsp; We can run FreeSurfer 6.0 fine, but they say there are differences between the versions. &nbsp;1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0-full
>>>> 2) Platform: Ubuntu 18.04.1 LTS
>>>> 3) uname -a: Linux clps-pb1 4.15.0-64-generic #73-Ubuntu SMP Thu Sep 12 13:16:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>>>> 4) recon-all.log: n/a Segmentation Fault - see below(base) root@clps-pb1:/var/tmp# cd freesurfer4(base) root@clps-pb1:/var/tmp/freesurfer4# lsASegStatsLUT.txt &nbsp;DefectLUT.txt &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; FreeSurferEnv.sh &nbsp;mni &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Simple_surface_labels2009.txtAUTHORS &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; diffusion &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; fsafd &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; SegmentNoLUT.txt &nbsp; &nbsp; subjectsaverage &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; docs &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;fsfast &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;sessions &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; tkmeditParcColorsCMAbin &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; FreeSurferColorLUT.txt &nbsp;lib &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; SetUpFreeSurfer.cshbuild-stamp.txt &nbsp; FreeSurferEnv.csh &nbsp; &nbsp; &nbsp; matlab &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;SetUpFreeSurfer.sh(base) root@clps-pb1:/var/tmp/freesurfer4# export FREESURFER_HOME=/var/tmp/freesurfer4(base) root@clps-pb1:/var/tmp/freesurfer4# source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME &nbsp; /var/tmp/freesurfer4FSFAST_HOME &nbsp; &nbsp; &nbsp; /var/tmp/freesurfer4/fsfastFSF_OUTPUT_FORMAT niiSUBJECTS_DIR &nbsp; &nbsp; &nbsp;/var/tmp/freesurfer4/subjectsMNI_DIR &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; /var/tmp/freesurfer4/mni(base) root@clps-pb1:/var/tmp/freesurfer4# cd ..(base) root@clps-pb1:/var/tmp# cd f4bash: cd: f4: No such file or directory(base) root@clps-pb1:/var/tmp# mkdir f4(base) root@clps-pb1:/var/tmp# cd f4(base) root@clps-pb1:/var/tmp/f4# ls(base) root@clps-pb1:/var/tmp/f4# &nbsp;export SUBJECTS_DIR=/var/tmp/f4(base) root@clps-pb1:/var/tmp/f4# cp $FREESURFER_HOME/subjects/sample-001.mgz .(base) root@clps-pb1:/var/tmp/f4# ls -lrttotal 6136-rw-r--r-- 1 r!
 oo!
>> t r!
>>>> oot 6280
>>>> 209 Nov 19 15:13 sample-001.mgz(base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz sample-001.nii.gzmri_convert sample-001.mgz sample-001.nii.gz$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $reading from sample-001.mgz...Segmentation fault (core dumped)(base) root@clps-pb1:/var/tmp/f4#Thanks,Paulo_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> -------------- next part --------------
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>>>>
>>>> ------------------------------
>>>>
>>>> Message: 11
>>>> Date: Thu, 21 Nov 2019 09:34:36 +0000
>>>> From: Aline Delva <aline.delva@uzleuven.be>
>>>> Subject: [Freesurfer] Substantia nigra delineation
>>>> To: "'freesurfer@nmr.mgh.harvard.edu'"
>>>>     <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <4152f89856664506bc9122d2dd6684c5@uzleuven.be>
>>>> Content-Type: text/plain; charset="ks_c_5601-1987"
>>>>
>>>>         External Email - Use Caution
>>>>
>>>> Dear,
>>>>
>>>> We would like to delineate the substantia nigra using a 3D Sag BRAVO and a 3D Sag FLAIR in freesurfer.
>>>> What is the optimal method to do this?
>>>> We already performed recon all and unfortunately SN was not segmented.
>>>>
>>>> Yours sincerely,
>>>>
>>>> Delva Aline, MD
>>>>
>>>> Neurology resident
>>>> UZ Leuven, Belgium
>>>> * aline.delva@uzleuven.be<mailto:aline.delva@uzleuven.be>
>>>>
>>>> PhD student Biomedical sciences
>>>> KU Leuven Department of Neurosciences, Research Group Experimental Neurology, Laboratory for Parkinson Research
>>>> KU Leuven Deparement of Imaging and Pathology, Nuclear Medicine and Molecular Imaging
>>>> * aline.delva@kuleuven.be<mailto:aline.delva@kuleuven.be>
>>>> ?   +32 (0) 16 345771
>>>>
>>>> -------------- next part --------------
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>>>>
>>>> ------------------------------
>>>>
>>>> Message: 12
>>>> Date: Thu, 21 Nov 2019 08:49:24 -0500
>>>> From: "Baptista, Paulo" <paulo_baptista@brown.edu>
>>>> Subject: Re: [Freesurfer] Freesurfer 4.5 on Ubuntu 18.04 ?
>>>> To: fsbuild <fsbuild@contbay.com>
>>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>>> Message-ID:
>>>>     <CAMKPAzhYH_WMS3UcXEZ+Q5zS7xsGWUbEr5kKGV_C_gRDQEtAzA@mail.gmail.com>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>>         External Email - Use Caution
>>>>
>>>> Hello--
>>>>
>>>> Good morning.  Thank you very much for your email.
>>>>
>>>> Yes we have the license file.  When we didn't have the license file, we
>>>> would get an error about missing license file.
>>>>
>>>> (base) pbaptist@clps-pb1:/var/tmp/freesurfer4$ ls
>>>> ASegStatsLUT.txt  bin              diffusion
>>>> FreeSurferEnv.csh  fsfast  mni               SetUpFreeSurfer.csh
>>>> subjects
>>>> AUTHORS           build-stamp.txt  docs                    FreeSurferEnv.sh
>>>>   lib     SegmentNoLUT.txt  SetUpFreeSurfer.sh
>>>> tkmeditParcColorsCMA
>>>> average           DefectLUT.txt    FreeSurferColorLUT.txt  fsafd
>>>>    matlab  sessions          Simple_surface_labels2009.txt
>>>> (base) pbaptist@clps-pb1:/var/tmp/freesurfer4$ ls -la .license
>>>> -rw-r--r-- 1 root root 49 Nov 18 15:10 .license
>>>> (base) pbaptist@clps-pb1:/var/tmp/freesurfer4$ cat .license
>>>> pb@brown.edu
>>>> 41878
>>>> *C8f07l/gczz6
>>>> FSdMgckdPeGoE
>>>> (base) pbaptist@clps-pb1:/var/tmp/freesurfer4$
>>>>
>>>> (base) root@clps-pb1:/var/tmp/freesurfer4# mv .license license
>>>> (base) root@clps-pb1:/var/tmp/freesurfer4# cd bin
>>>> (base) root@clps-pb1:/var/tmp/freesurfer4/bin#  export
>>>> FREESURFER_HOME=/var/tmp/freesurfer4
>>>> (base) root@clps-pb1:/var/tmp/freesurfer4/bin# source
>>>> $FREESURFER_HOME/SetUpFreeSurfer.sh
>>>> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 --------
>>>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>>> FREESURFER_HOME   /var/tmp/freesurfer4
>>>> FSFAST_HOME       /var/tmp/freesurfer4/fsfast
>>>> FSF_OUTPUT_FORMAT nii
>>>> SUBJECTS_DIR      /var/tmp/freesurfer4/subjects
>>>> MNI_DIR           /var/tmp/freesurfer4/mni
>>>> (base) root@clps-pb1:/var/tmp/freesurfer4/bin# export
>>>> SUBJECTS_DIR=/var/tmp/f4
>>>> (base) root@clps-pb1:/var/tmp/freesurfer4/bin# cd  /var/tmp/f4
>>>> (base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz
>>>> sample-001.nii.gz
>>>> mri_convert sample-001.mgz sample-001.nii.gz
>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>> reading from sample-001.mgz...
>>>> --------------------------------------------------------------------------
>>>> *ERROR: FreeSurfer license file /var/tmp/freesurfer4/.license not found.*
>>>>   If you are outside the NMR-Martinos Center,
>>>>   go to http://surfer.nmr.mgh.harvard.edu to
>>>>   get a valid license file (it's free).
>>>>   If you are inside the NMR-Martinos Center,
>>>>   make sure to source the standard environment.
>>>> --------------------------------------------------------------------------
>>>> (base) root@clps-pb1:/var/tmp/f4#
>>>>
>>>> *(base) root@clps-pb1:/var/tmp/f4# mv /var/tmp/freesurfer4/license
>>>> /var/tmp/freesurfer4/.license*
>>>> (base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz
>>>> sample-001.nii.gz
>>>> mri_convert sample-001.mgz sample-001.nii.gz
>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>> reading from sample-001.mgz...
>>>> *Segmentation fault (core dumped)*
>>>> (base) root@clps-pb1:/var/tmp/f4#
>>>>
>>>>
>>>> Ok, will you confirm Ubuntu 18 can not run Freesurfer 4?
>>>>
>>>> Thanks,
>>>>
>>>> Paulo
>>>>
>>>>
>>>> On Thu, Nov 21, 2019 at 1:14 AM fsbuild <fsbuild@contbay.com> wrote:
>>>>
>>>>> Hello Paulo,
>>>>>
>>>>> What is the location of the freesurfer license file (?), i.e., I would
>>>>> make sure the freesurfer license file is under $FREESURFER_HOME and then
>>>>> see if you get different results running the command.
>>>>>
>>>>> Even with the license file though, I?m not sure all the Freesurfer 4
>>>>> binaries will run on Ubuntu 18
>>>>>
>>>>> - R.
>>>>>
>>>>> On Nov 19, 2019, at 15:26, Baptista, Paulo <paulo_baptista@brown.edu>
>>>>> wrote:
>>>>>
>>>>>         External Email - Use Caution
>>>>>
>>>>> Hello FreeSurfer Developers,
>>>>>> I am helping a researcher in my department run FreeSurfer on a new
>>>>>> computer..  They insist that it should run on FreeSurfer 4.5 because their
>>>>>> old system ran that version.  Is the following possible?  We can run
>>>>>> FreeSurfer 6.0 fine, but they say there are differences between the
>>>>>> versions.
>>>>>>
>>>>>> 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0-full
>>>>>> 2) Platform: Ubuntu 18.04.1 LTS
>>>>>> 3) uname -a: Linux clps-pb1 4..15.0-64-generic #73-Ubuntu SMP Thu Sep 12 13:16:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>>>>>> 4) recon-all.log: n/a Segmentation Fault - see below
>>>>>>
>>>>>> (base) root@clps-pb1:/var/tmp# cd freesurfer4
>>>>>> (base) root@clps-pb1:/var/tmp/freesurfer4# ls
>>>>>> ASegStatsLUT.txt  DefectLUT.txt           FreeSurferEnv.sh  mni
>>>>>>        Simple_surface_labels2009.txt
>>>>>> AUTHORS           diffusion               fsafd
>>>>>> SegmentNoLUT.txt     subjects
>>>>>> average           docs                    fsfast            sessions
>>>>>>         tkmeditParcColorsCMA
>>>>>> bin               FreeSurferColorLUT.txt  lib
>>>>>> SetUpFreeSurfer.csh
>>>>>> build-stamp.txt   FreeSurferEnv.csh       matlab
>>>>>> SetUpFreeSurfer.sh
>>>>>> (base) root@clps-pb1:/var/tmp/freesurfer4# export

>>>>>> FREESURFER_HOME=/var/tmp/freesurfer4
>>>>>> (base) root@clps-pb1:/var/tmp/freesurfer4# source
>>>>>> $FREESURFER_HOME/SetUpFreeSurfer.sh
>>>>>> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 --------
>>>>>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>>>>> FREESURFER_HOME   /var/tmp/freesurfer4
>>>>>> FSFAST_HOME       /var/tmp/freesurfer4/fsfast
>>>>>> FSF_OUTPUT_FORMAT nii
>>>>>> SUBJECTS_DIR      /var/tmp/freesurfer4/subjects
>>>>>> MNI_DIR           /var/tmp/freesurfer4/mni
>>>>>> (base) root@clps-pb1:/var/tmp/freesurfer4# cd ..
>>>>>> (base) root@clps-pb1:/var/tmp# cd f4
>>>>>> bash: cd: f4: No such file or directory
>>>>>> (base) root@clps-pb1:/var/tmp# mkdir f4
>>>>>> (base) root@clps-pb1:/var/tmp# cd f4
>>>>>> (base) root@clps-pb1:/var/tmp/f4# ls
>>>>>> (base) root@clps-pb1:/var/tmp/f4#  export SUBJECTS_DIR=/var/tmp/f4
>>>>>> (base) root@clps-pb1:/var/tmp/f4# cp
>>>>>> $FREESURFER_HOME/subjects/sample-001.mgz .
>>>>>> (base) root@clps-pb1:/var/tmp/f4# ls -lrt
>>>>>> total 6136
>>>>>> -rw-r--r-- 1 root root 6280209 Nov 19 15:13 sample-001.mgz
>>>>>> (base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz
>>>>>> sample-001.nii.gz
>>>>>> mri_convert sample-001.mgz sample-001.nii.gz
>>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>>>> reading from sample-001.mgz...
>>>>>> Segmentation fault (core dumped)
>>>>>> (base) root@clps-pb1:/var/tmp/f4#
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Paulo
>>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>
>>>>>
>>>> -------------- next part --------------
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>>>>
>>>> ------------------------------
>>>>
>>>> Message: 13
>>>> Date: Thu, 21 Nov 2019 10:03:04 -0500
>>>> From: An <annaqu1024@gmail.com>
>>>> Subject: [Freesurfer] Map fMRI data onto surface
>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID:
>>>>     <CAJVCUNc8kM2EFuH_csYPTJcNcb1pPVtfa9Dwjq=7HAS4J8qkiA@mail.gmail.com>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>>         External Email - Use Caution
>>>>
>>>> Hi there,
>>>>
>>>> I want to map the intensities of the fMRI 4D volumes onto its surface in
>>>> order to get the functional values on each vertex in each frame.
>>>>
>>>> I have done the following steps for achieving this:
>>>> 1. ran recon-all on its anatomical volume.
>>>> 2. register the fMRI series with the anatomical volume by using bbregister.
>>>> 3. assign values from volumes to each surface vertex through the command
>>>> mri_vol2surf.
>>>>
>>>> I have got a result of mapping the 4D volumes intensities onto its surfaces
>>>> but there are 35.5% vertices assigned 0 value in every time frame.
>>>>
>>>> I am wondering is the ratio reasonable and how could I improve the result?
>>>> I guess resolution would be one of reasons causing the high 0 value ratio,
>>>> my fMRI data is 2mm^3 and anatomical data is 1mm^3.
>>>>
>>>> Many thanks for your help.
>>>>
>>>> Best,
>>>> An
>>>> -------------- next part --------------
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>>>>
>>>> ------------------------------
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>> End of Freesurfer Digest, Vol 189, Issue 29
>>>> *******************************************
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Tue, 26 Nov 2019 22:14:26 +0000
>> From: "Billah, Tashrif" <tbillah@bwh.harvard.edu>
>> Subject: [Freesurfer] [recon-all] [use of -T2] Does only -autorecon3
>>       use -T2?
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID:
>>       <CY1PR04MB237735593A9238A8F072D2CFFF450@CY1PR04MB2377.namprd04.prod.outlook.com>
>>      
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi all,
>>
>> Is -T2 used only in -autorecon3 as shown here<https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Other>:
>>
>> recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3
>>
>> In other words, if I do:
>>
>> recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume -T2pial -all
>>
>> Will only -autorecon3 make use of the provided -T2 and not -autorecon1 or -autorecon2?
>>
>> I think the answers are yes because -T2 appears under -autorecon3 only in ReconAllDevTable<https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable>.
>>
>> Best,
>> Tashrif
>>
>>
>> -------------------------------------------------------------
>>
>> Tashrif Billah, MS<https://www.linkedin.com/in/tashrif-billah/>
>>
>> Research Engineer
>>
>> Brigham and Women's Hospital
>>
>> Harvard Medical School
>>
>> tbillah@bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu>
>>
>> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 7
>> Date: Tue, 26 Nov 2019 23:07:02 +0000
>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] extract lgi
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <9695fac1-9a73-040c-4d28-53bf535f0466@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> yes, see
>> https://surfer.nmr.mgh.harvard.edu/fswiki/LGI
>>
>> On 11/26/2019 2:07 AM, An Lijun wrote:
>>
>>         External Email - Use Caution
>>
>> Dear Yanyan,
>> Actually you could refer to the freesurfer tutorial firstly.
>>
>> Best Regards,
>> An Lijun
>>
>>
>> Lin Yanyan <linyanyan@outlook.com<mailto:linyanyan@outlook.com>> ?2019?11?26??? ??12:49???
>>
>>         External Email - Use Caution
>>
>> Hello, I have a question about lgi computing and extracting. I had run recon-all -s <subjid> -all, and there are lh.pail/rh.pail under each subject, then what should I do?
>>
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191126/7f0dd2c6/attachment-0001.html
>>
>> ------------------------------
>>
>> Message: 8
>> Date: Tue, 26 Nov 2019 23:09:04 +0000
>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] [recon-all] [use of -T2] Does only
>>       -autorecon3 use -T2?
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <023e58ce-1ba1-44c9-a07b-5582d1f76957@mgh.harvard.edu>
>> Content-Type: text/plain; charset="windows-1252"
>>
>> Yes, the T2 is only used to refine the pial surface
>>
>> On 11/26/2019 5:14 PM, Billah, Tashrif wrote:
>> Hi all,
>>
>> Is -T2 used only in -autorecon3 as shown here<https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Other>:
>>
>> recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3
>>
>> In other words, if I do:
>>
>> recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume -T2pial -all
>>
>> Will only -autorecon3 make use of the provided -T2 and not -autorecon1 or -autorecon2?
>>
>> I think the answers are yes because -T2 appears under -autorecon3 only in ReconAllDevTable<https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable>.
>>
>> Best,
>> Tashrif
>>
>>
>> -------------------------------------------------------------
>>
>> Tashrif Billah, MS
>>
>> Research Engineer
>>
>> Brigham and Women's Hospital
>>
>> Harvard Medical School
>>
>> tbillah@bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu>
>>
>> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 9
>> Date: Tue, 26 Nov 2019 23:12:57 +0000
>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] PetSurfer questions
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <b3bf802b-6ee4-bd7e-486f-ba651d7d9efb@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> what ligand are you using? Do you expect it to be higher in GM and in WM? What are the values in the gtm.stats file relative to when you run it without PVC? How did you choose 5 as the --psf?
>>
>> On 11/26/2019 2:53 AM, Soo-Jong Kim wrote:
>>
>>         External Email - Use Caution
>>
>> Dear FreeSurfer experts,
>>
>> Originally, I want to use RBV method for pvcorrected PET for SUVR analysis.
>>
>> After generating gtmseg and coregistration to make lta file, I followed this code and changed some.
>>
>> mri_gtmpvc --i PET.nii --reg subj1.reg.lta --psf 5 --seg gtmseg.mgz
>> --default-seg-merge --auto-mask PSF .01 --no-rescale --no-reduce-fov --rbv --o output_pvc
>>
>> After this, rbv.nii.gz file was generated. and SUVR analysis was performed as reference region (cerebellar cortex).  But Compared to original un-pvc PET, Cortex SUVR was reduced.
>>
>> In ideal pv-corrected PET, cortex SUVR was higher than un-pvc PET.
>>
>> Is is okay if I use the output file as rbv.nii.gz ?
>>
>> in Thomas et al, 2011,
>> He used aparc+aseg.mgz file from FreeSurfer. and he merged some regions.
>> Frontal, Temporal, Occipital and so on. (Only gray matter to correct PET using RBV method)
>>
>> In that case, What are the regions to make rbv.nii.gz method in PetSurfer?  all regions in FreeSurfer LUT?
>>
>> Can I use the rbv.nii.gz as partial volume corrected PET from RBV method?
>>
>> If not, let me know what is the correct command of mri_gtmpvc.
>> I need only partial volume corrected PET using RBV method.
>>
>> Sincerely,
>>
>> Soo-Jong Kim
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
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>>
>> ------------------------------
>>
>> Message: 10
>> Date: Tue, 26 Nov 2019 23:14:06 +0000
>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>> Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster
>>       summary file
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID: <45927090-1c88-9f64-351a-e930cc3d3097@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> can you send the cluster summary file?
>>
>> On 11/24/2019 7:09 PM, Bronwyn Overs wrote:
>>
>>         External Email - Use Caution
>>
>> Hi Kersten,
>>
>> Following on from Douglas's reply, you may remember my analysis as I forwarded you some files in October (see https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64148.html). I followed your suggestions of removing the '--thmax 5' argument form 'mri_surfcluster', and now the labels generated by 'mri_label2label' overlap perfectly with the significance maps from the LME. However, now my largest clusters have a maximum threshold of '-inf' in my cluster summary files. Do you have any idea how to get around this problem so that I can use my max threshold values to calculate cluster-wise effect sizes?
>>
>>
>>
>> Kind regards,
>>
>>
>> Bronwyn Overs
>>
>> Research Assistant
>>
>> [cid:part2.69D05ACA.AA1EE7B5@mgh.harvard.edu]
>>
>>
>> Neuroscience Research Australia
>> Margarete Ainsworth Building
>> Barker Street Randwick Sydney NSW 2031 Australia
>> M 0411 308 769 T +61 2 9399 1725
>>
>>
>> neura.edu.au <http://neura.edu.au/>
>>
>>
>> Twitter<https://twitter.com/neuraustralia> | Facebook<https://www.facebook.com/NeuroscienceResearchAustralia> | Subscribe<http://www.neura.edu.au/help-research/subscribe>
>>
>>
>>
>> ________________________________
>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu><mailto:DGREVE@mgh.harvard.edu>
>> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>, "Kersten Diers, DZNE" <Kersten.Diers@dzne.de><mailto:Kersten.Diers@dzne.de>
>> Sent: Thursday, November 14, 2019 4:23:12 AM
>> Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file
>>
>> I'll have to leave this one for Kersten as it appears that the LME stuff
>> is generating and inf value
>>
>> On 11/12/19 7:05 PM, Bronwyn Overs wrote:
>>>         External Email - Use Caution
>>>
>>> Hi Douglas,
>>>
>>> Yes I have looked at it in Freeview and I have attached a screenshot
>>> for your reference.
>>>
>>> The /fsdata/lme/thickness/rh.thickness.B1B7.mgh file was generated
>>> with a mass-univariate spatiotemporal model using
>>> 'lme_mass_fit_EMinit' and then FDR correction was applied across both
>>> hemispheres (lme_mass_FDR). I have provided analysis details and
>>> syntax below. The B1B7 contrast represents the affect of years in cases.
>>>
>>> Sample:
>>> Our sample includes 112 controls subjects, and 106 cases. All subjects
>>> are aged between 12 and 30 years. 153 or these subjects have 2
>>> time-points (77 control, 76 cases), while the remaining 65 individuals
>>> have only 1 MRI time-point. We also have mixed ethnicites - 165
>>> Caucasians, 23 Asians, and 30 mixed (Asians-Caucasians).
>>>
>>> The QDEC file contains the following 6 variables:
>>> 1. Y (years between scans)
>>> 2. A (baseline age)
>>> 3. G (group, 1=case, 0=control)
>>> 4. S (sex, 1=female, 0=male)
>>> 5. E1 (Ethnicity 1, 1=asian, 0=other)
>>> 6. E2 (Ethnicity 1, 1=mixed-asian-caucasian, 0=other)
>>>
>>> Design matrix: [ones(length(M),1) M M(:,1).*M(:,3)]
>>>                i.e. main effects for each of the qdec variables + an
>>> interaction term for years X group
>>>
>>> DVs: Cortical thickness, area and volume
>>>
>>> Model: Mass-univariate spatiotemporal model using
>>> 'lme_mass_fit_EMinit'
>>> CODE:
>>>   % Read in surface files
>>>   [Y,mri] = fs_read_Y(mgh);
>>>   % Read in qdec file
>>>   Qdec = fReadQdec(qdec);
>>>   % Remove fsid from qdec
>>>   Qdec = rmQdecCol(Qdec,1);
>>>   % Store col 1 (fsid-base) in sID variable
>>>   sID = Qdec(2:end,1);
>>>   % Remove col 1 (fsid-base) from Qdec array
>>>   Qdec = rmQdecCol(Qdec,1);
>>>   % Convert Qdec to numeric matrix M
>>>   M = Qdec2num(Qdec);
>>>   % Sort data and evaluate design matrix
>>>   [M,Y,ni] = sortData(M,1,Y,sID);
>>>   X = eval([ones(length(M),1) M M(:,1).*M(:,3)])
>>>   % Compute vertex-wise temporal covariance estimates.
>>>   [Th0, Re] = lme_mass_fit_EMinit(X,[1],Y,ni,cortex,3);
>>>   %Segmentation and model fitting.
>>>   [Rgs, RgMeans, stats] = fit(Th0, Re, [1], sphere, cortex, X, Y,
>>> ni);
>>>   %Check surfaces.
>>>   surfcomp(Th0, RgMeans, sphere, fig1, fig2)
>>>
>>> Correction for multiple comparisons: FDR across both hemispheres
>>> CODE:
>>>   P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ]; G = [
>>> F_lhstats.sgn(lhcortex)
>>>   F_rhstats.sgn(rhcortex) ];
>>>   [detvtx, sided_pval, pth] = lme_mass_FDR2(P,G,[],0.05,0);
>>>   altfdr(r,2) = num2cell(abs(log10(lme_mass_FDR(P,0.05))));
>>>   pcor = -log10(pth);
>>>   [~,~,dflh] = find(F_lhstats.df(2,:));
>>>   [~,~,dfrh] = find(F_rhstats.df(2,:));
>>>   dfmodelh(r,2) = {floor(mode(dflh))};
>>>   dfmoderh(r,2) = {floor(mode(dfrh))};
>>>   thrlh(r,2) = {pcor};
>>>   thrrh(r,2) = {pcor};
>>>   [~,dc] = size(detvtx);
>>>   dvtx(r,2) = {dc};
>>>
>>> Kind regards,
>>>
>>>
>>> Bronwyn Overs
>>>
>>> Research Assistant
>>>
>>>
>>> Neuroscience Research Australia
>>> Margarete Ainsworth Building
>>> Barker Street Randwick Sydney NSW 2031 Australia
>>> *M* 0411 308 769 *T* +61 2 9399 1725
>>>
>>>
>>> neura.edu.au <http://neura.edu.au/><http://neura.edu.au/>
>>>
>>> Twitter <https://twitter.com/neuraustralia><https://twitter.com/neuraustralia> | Facebook
>>> <https://www.facebook.com/NeuroscienceResearchAustralia><https://www.facebook.com/NeuroscienceResearchAustralia> | Subscribe
>>> <http://www.neura.edu.au/help-research/subscribe><http://www.neura.edu.au/help-research/subscribe>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>> *From: *"Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu><mailto:DGREVE@mgh.harvard.edu>
>>> *To: *"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
>>> *Sent: *Wednesday, November 13, 2019 2:44:25 AM
>>> *Subject: *Re: [Freesurfer] Max threshold marked as '-inf' in cluster
>>> summary file
>>>
>>> It looks like you have one gigantic cluster with a value of -inf at
>>> vertex 41. How did you generate
>>> /fsdata/lme/thickness/rh.thickness.B1B7.mgh ? Have you looked at it in
>>> freeview?
>>>
>>> On 11/11/2019 7:39 PM, Bronwyn Overs wrote:
>>>
>>>             External Email - Use Caution
>>>
>>>     Dear Freesurfer Mailing List,
>>>
>>>     I have completed an LME analysis in matlab and have generated a
>>>     number of different cluster summary files for my various
>>>     contrasts. In many of resulting cluster summary files the 'Max'
>>>     value for the largest cluster which encompasses most of the brain
>>>     surface is reported as infinity ('-inf'). Please find an example
>>>     file attached. As I was hoping to use these values to generate
>>>     effect size estimates, can you please tell me what alternate value
>>>     I could substitute here for 'Max'?
>>>
>>>     Kind regards,
>>>
>>>
>>>     Bronwyn Overs
>>>
>>>     Research Assistant
>>>
>>>
>>>     Neuroscience Research Australia
>>>     Margarete Ainsworth Building
>>>     Barker Street Randwick Sydney NSW 2031 Australia
>>>     *M* 0411 308 769 *T* +61 2 9399 1725
>>>
>>>
>>>     neura.edu.au <http://neura.edu.au/><http://neura.edu.au/>
>>>
>>>     Twitter <https://twitter.com/neuraustralia><https://twitter.com/neuraustralia> | Facebook
>>>     <https://www.facebook.com/NeuroscienceResearchAustralia><https://www.facebook.com/NeuroscienceResearchAustralia> |
>>>     Subscribe <http://www.neura.edu.au/help-research/subscribe><http://www.neura.edu.au/help-research/subscribe>
>>>
>>>
>>>
>>>
>>>     _______________________________________________
>>>     Freesurfer mailing list
>>>     Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>  <mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
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>>
>> ------------------------------
>>
>> Message: 11
>> Date: Wed, 27 Nov 2019 11:34:14 +0000
>> From: "Ferraro, Pilar" <FerraroP@pennmedicine.upenn.edu>
>> Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue
>>       34
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Message-ID:
>>       <C7924C62-27B6-4A60-A8A0-FCB8DFBF44C4@pennmedicine.upenn.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>>         External Email - Use Caution
>>
>> Hi Freesurfer experts,
>>
>> I?ve sent this email but I did not receive any reply on the thread.
>> Should I post it again?
>>
>> Many thanks to you all,
>>
>> Pilar Ferraro
>>> ------------------------------
>>>
>>> Message: 3
>>> Date: Mon, 25 Nov 2019 11:42:24 +0000
>>> From: "Ferraro, Pilar" <FerraroP@pennmedicine.upenn.edu>
>>> Subject: [Freesurfer] Regression analysis correcting for 1 variable
>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID:
>>>      <577C5915-60F4-46E6-BED5-1E592B3CD41F@pennmedicine.upenn.edu>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>>        External Email - Use Caution
>>>
>>> Hi Freesurfer experts,
>>>
>>> I?ve received your last response concerning the cortical thickness comparison between patients and HC correcting for disease duration and I?ve successfully completed the procedure.
>>> Thanks again!
>>> Now I?m contacting you cause I?m running a different analysis and I?m struggling to understand how to proceed.
>>> In particular I would like to complete a regression analysis (only in patients, therefore only one group) looking at the effect of Variable X on cortical thickness (which I assume being higher X values corresponding to lower CT values), correcting for the effect of Variable Y (disease duration).
>>> When I?ve looked at the Freesurfer Wiki for finding good examples I?ve thought I can use the one group, two covariates example.
>>> However, in this case I?m not sure how the FSGD file and the matrix should be organized.
>>> I suppose the FSGD file can simply list the Input subjects, Variable X and Variable Y.
>>> Then the matrix should be 0 -1 0.
>>> Am I correct?
>>>
>>> Thanks for any help!
>>>
>>> Pilar Ferraro
>>>
>>>
>>>
>>>> ------------------------------
>>>>
>>>> Message: 3
>>>> Date: Wed, 20 Nov 2019 22:40:29 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] Fwd: surface group analysis with qdec
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <70fa9541-d854-4530-9180-d001cf008f04@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> I responded to this a few days ago. Below is what I said
>>>>
>>>> The problem is that all of your class=0 subjects have a 0 duration
>>>> meaning that you cannot compute a duration slope for this class. In this
>>>> special case, you can run a different-offset, same-slope analysis with
>>>> --fsgd dur.fsgd doss
>>>> Change your contrast matrix to 1 -1 0
>>>>
>>>>
>>>> On 11/19/19 5:00 AM, Ferraro, Pilar wrote:
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> Hi,
>>>>>
>>>>> I?ve never got a response to my last email (you can find it below).
>>>>>
>>>>> Would you be able to let me know so I can proceed with the analyses?
>>>>>
>>>>> Many thanks,
>>>>>
>>>>> Pilar
>>>>>
>>>>>> Inizio messaggio inoltrato:
>>>>>>
>>>>>> *Da: *"Ferraro, Pilar" <FerraroP@pennmedicine.upenn.edu
>>>>>> <mailto:FerraroP@pennmedicine.upenn.edu>>
>>>>>> *Oggetto: **Fw: surface group analysis with qdec*
>>>>>> *Data: *14 novembre 2019 3:47:42 PM CET
>>>>>> *A: *"freesurfer@nmr.mgh.harvard.edu
>>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>"
>>>>>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I'm trying to run a surface based group analysis comparing patients
>>>>>> and HC, correcting for disease duration.
>>>>>> I enclose here the fsgd file and the design matrix.
>>>>>> I've followed all the steps of the tutorial
>>>>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0)?with
>>>>>> no errors.
>>>>>> However, when I try to run the glm analysis with the following command:
>>>>>>
>>>>>> mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C
>>>>>> lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir
>>>>>> lh.dur.glmdir
>>>>>>
>>>>>> I get the error:
>>>>>>
>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>>>>>> --------------------------------
>>>>>> Possible problem with experimental design:
>>>>>> Check for duplicate entries and/or lack of range of
>>>>>> continuous variables within a class.
>>>>>>
>>>>>> Of course there is no range for the continuous variable (disease
>>>>>> duration) in the control group, so I'm wondering how to overcome
>>>>>> this?limit and proceed correctly with the glm analysis.
>>>>>>
>>>>>> Many thanks in advance for any help you will provide,
>>>>>>
>>>>>> Pilar
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------
>>>>>> *From:*Ferraro, Pilar
>>>>>> *Sent:*Monday, November 11, 2019 7:07 AM
>>>>>> *To:*freesurfer@nmr.mgh.harvard.edu
>>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>>>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>>>> *Subject:*surface group analysis with qdec
>>>>>> Hi!
>>>>>>
>>>>>> I've previously run a comparison between patients and HC using qdec,
>>>>>> but now I'd like to correct the analysis for disease duration.
>>>>>> I've therefore generated a second qdec.table.dat file inserting the
>>>>>> disease duration column with the following structure:
>>>>>> fsid group duration
>>>>>> Input subj1 1 13
>>>>>> Input subj2 0
>>>>>>
>>>>>> (For healthy controls group (group 0) I've tried both options,
>>>>>> leaving the duration column blank or inserting 0 as a value).
>>>>>> I've also left the group.level file the same of the previous analysis.
>>>>>> However, when i open the new qdec.table.dat file with qdec I get
>>>>>> problems in correctly uploading the data.
>>>>>> In particular, I get the following error:
>>>>>>
>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>>>>>> Possible problem with experimental design:
>>>>>> Check for duplicate entries and/or lack of range of continuous
>>>>>> variables within a class.
>>>>>> If you seek help with this problem, make sure to send:
>>>>>> ?This is the command line:
>>>>>> ?mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh
>>>>>> --fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods
>>>>>> --glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage
>>>>>> lh --label
>>>>>> /home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C
>>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
>>>>>> --C
>>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat
>>>>>>
>>>>>> Of course there is no range for the continuous variable (disease
>>>>>> duration) in the control group, so I'm wondering how to overcome this
>>>>>> and generate a?correct qdec.table.dat file.
>>>>>>
>>>>>> Thanks in advance for any help!
>>>>>>
>>>>>> Pilar
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 4
>>>> Date: Wed, 20 Nov 2019 22:45:18 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] Question about the input for longitudinal
>>>>     processing pipeline
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <8be29ed9-8627-d005-fd9b-ca3ec56f8a5b@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> I have not run images with contrast, but I think it should? work. Some
>>>> people have tried to use the mp2rage UNI scan, but it often fails
>>>> because of very bright voxels outside of the brain. If you can remove
>>>> those (eg, skull stripping), then it might work. Alternatively, if you
>>>> have a quantitative T1 that comes out of the mp2rage if you have the
>>>> license, then you can simulate an mp1rage that will then work in FS (but
>>>> it will have bias fields). If you don't have a qT1, it is not too hard
>>>> to convert the UNI to qT1. Is this at 3T or 7t?
>>>>
>>>> On 11/19/19 5:35 AM, Darko Komneni? wrote:
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> Hi Douglas,
>>>>> thanks for your reply. Indeed, in this particular data set they don't
>>>>> all have contrast, which is unfortunate. But my question was also
>>>>> general, if we assume that they all have contrast, would it be OK to
>>>>> use those images as inputs in the longitudinal pipeline? And the same
>>>>> question for mp2rage images, are they OK to use as well, or are they
>>>>> not suitable for this pipeline?
>>>>> Best,
>>>>> Darko
>>>>>
>>>>>
>>>>>   ------------------------------
>>>>>
>>>>>   Message: 11
>>>>>   Date: Mon, 18 Nov 2019 18:41:37 +0000
>>>>>   From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu
>>>>>   <mailto:DGREVE@mgh.harvard.edu>>
>>>>>   Subject: Re: [Freesurfer] Question about the input for longitudinal
>>>>>   ? ? ? ? processing pipeline
>>>>>   To: "freesurfer@nmr.mgh.harvard.edu
>>>>>   <mailto:freesurfer@nmr.mgh.harvard.edu>"
>>>>>   <freesurfer@nmr.mgh.harvard.edu
>>>>>   <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>>>   Message-ID: <d5205fe6-329a-f9b4-252a-8f1857aa42e4@mgh.harvard.edu
>>>>>   <mailto:d5205fe6-329a-f9b4-252a-8f1857aa42e4@mgh.harvard.edu>>
>>>>>   Content-Type: text/plain; charset="utf-8"
>>>>>
>>>>>   Do all images and time points have contrast? If some do and some
>>>>>   don't,
>>>>>   then I don't think you can properly do the analysis?
>>>>>
>>>>>   On 11/15/19 10:06 AM, Darko Komneni? wrote:
>>>>>> ????????External Email - Use Caution
>>>>>>
>>>>>> Dear Freesurfer experts,
>>>>>> I wanted to run the Freesurfer's longitudinal processing pipeline
>>>>>> (described here
>>>>>>
>>>>>   https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing)
>>>>>   on a
>>>>>> series of MRI scans from a single patient. However, after
>>>>>   looking at
>>>>>> the scans, i realized that for most time points, the patient
>>>>>   doesn't
>>>>>> have a "simple/normal" T1 MPRAGE sequence available. Instead, they
>>>>>> have a T1 sequence with a contrast agent, as well as T1 mp2rage
>>>>>> sequences.
>>>>>>
>>>>>> Is it possible/advisable to run recon-all in general or this
>>>>>   pipeline
>>>>>> in particular on T1 MPRAGE scans that have a contrast agent, or
>>>>>   that
>>>>>> are mp2rage instead of MPRAGE?
>>>>>>
>>>>>> Thanks in advance!
>>>>>> Best,
>>>>>> Darko
>>>>>>
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 5
>>>> Date: Wed, 20 Nov 2019 22:46:22 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] Local Gyrification Index: freesurfer version
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <2601bc80-e87a-74b3-9227-24ca60dafd97@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> It has not changed (and is no longer supported)
>>>>
>>>> On 11/19/19 6:48 AM, Steve Petersen wrote:
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> Dear Freesurfer experts,
>>>>>
>>>>> What freesurfer version do you recommend to perform the local
>>>>> gyrification index, version 6 or 6 development version?
>>>>>
>>>>>
>>>>> Thanks in advance.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 6
>>>> Date: Wed, 20 Nov 2019 22:51:21 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] Recon-all Error
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <13cb3ba0-0342-6f84-2029-2d4ac0eb914e@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> This is something that is being triggered by use -3T. Is there a reason
>>>> you are using that option?
>>>>
>>>> On 11/19/19 5:15 PM, Meena M. Makary wrote:
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> Hi,
>>>>>
>>>>> I have been getting this error with one of my subjects Recon-all. I am
>>>>> attaching the recon-all log file. any help would be appreciated!
>>>>>
>>>>> Meena
>>>>>
>>>>> --
>>>>> ?
>>>>> *Meena M. Makary, Ph.D.*
>>>>> Assistant Professor|Cairo University <http://bmes.cufe.edu.eg/>
>>>>> Postdoctoral Fellow|Radiology, Harvard?Medical School
>>>>> <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550>
>>>>> Postdoctoral Fellow| Athinoula A. Martinos Center, MGH
>>>>> <https://www.nmr.mgh.harvard.edu/user/4550386>
>>>>> Career Development and Mentoring Manager | OHBM Student and Postdoc
>>>>> SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449>
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 7
>>>> Date: Wed, 20 Nov 2019 22:54:30 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] mask for cortical thickness
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <f95d9228-9445-09c0-90d9-48f16e5a41f1@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> Pass the mask you want to mri_glmfit with either --label or --mask
>>>> (depending on your format). You can convert the aparc to labels using
>>>> mri_annotation2label , then pick the label you want. In this case, you
>>>> cannot use --cache as that has been computed using whole hemi. You can
>>>> generate your own MC simulation, but the better way to do this is with
>>>> permutation. see
>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>>>>
>>>> On 11/20/19 4:47 PM, Gwang-Won Kim wrote:
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> Hi there,
>>>>> I would like to analyze clusterwise correction for multiple
>>>>> comparisons using masks (exsample; superior frontal cortex and?middle
>>>>> frontal cortex).
>>>>> I know that "2spaces" means adjust p-values for two hemispheres as
>>>>> follow; mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 2 abs
>>>>> --2spaces.
>>>>> If I use the masks such as the superior frontal cortex and?middle
>>>>> frontal cortex,?how do I do?
>>>>> Thanks,
>>>>> Gwang-Won
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 8
>>>> Date: Wed, 20 Nov 2019 22:58:17 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue
>>>>     26
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <453c8556-e0de-cf0e-f84b-65c5273e186e@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> Sorry, I don't have your fsgd file anymore. It will be computing
>>>> FirstClass-SecondClass, so red means FirstClass>SecondClass
>>>>
>>>> On 11/19/19 6:05 AM, Ferraro, Pilar wrote:
>>>>>        External Email - Use Caution
>>>>>
>>>>> Thank you very much for your helpful reply!
>>>>> I?ve kept the same fsgd file, and just edited the contrast matrix to 1 -1 0 and added the doss option to the command line, as you suggested.
>>>>> I?m just a little bit confused cause now I get by default blue and red regions when I visualize the results in Freeview. Am I correct assuming that blue regions are the ones where cortical thickness is reduced in patients relative to HC correcting for disease duration?
>>>>> I just wanted to ask for a confirmation since in my fsgd file class 1 (patients) comes first and then class 0 (hc).
>>>>>
>>>>> Many thanks,
>>>>>
>>>>> Pilar
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 6
>>>>>> Date: Mon, 18 Nov 2019 18:28:58 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] Fw: surface group analysis with qdec
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <b967bd8b-5fb9-0c00-7207-3944fad5c09a@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="Windows-1252"
>>>>>>
>>>>>> The problem is that all of your class=0 subjects have a 0 duration
>>>>>> meaning that you cannot compute a duration slope for this class. In this
>>>>>> special case, you can run a different-offset, same-slope analysis with
>>>>>> --fsgd dur.fsgd doss
>>>>>> Change your contrast matrix to 1 -1 0
>>>>>>
>>>>>>
>>>>>> On 11/14/19 9:47 AM, Ferraro, Pilar wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I'm trying to run a surface based group analysis comparing patients
>>>>>>> and HC, correcting for disease duration.
>>>>>>> I enclose here the fsgd file and the design matrix.
>>>>>>> I've followed all the steps of the tutorial
>>>>>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0)?with
>>>>>>> no errors.
>>>>>>> However, when I try to run the glm analysis with the following command:
>>>>>>>
>>>>>>> mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C
>>>>>>> lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir
>>>>>>> lh.dur.glmdir
>>>>>>>
>>>>>>> I get the error:
>>>>>>>
>>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>>>>>>> --------------------------------
>>>>>>> Possible problem with experimental design:
>>>>>>> Check for duplicate entries and/or lack of range of
>>>>>>> continuous variables within a class.
>>>>>>>
>>>>>>> Of course there is no range for the continuous variable (disease
>>>>>>> duration) in the control group, so I'm wondering how to overcome
>>>>>>> this?limit and proceed correctly with the glm analysis.
>>>>>>>
>>>>>>> Many thanks in advance for any help you will provide,
>>>>>>>
>>>>>>> Pilar
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>> *From:* Ferraro, Pilar
>>>>>>> *Sent:* Monday, November 11, 2019 7:07 AM
>>>>>>> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
>>>>>>> *Subject:* surface group analysis with qdec
>>>>>>> Hi!
>>>>>>>
>>>>>>> I've previously run a comparison between patients and HC using qdec,
>>>>>>> but now I'd like to correct the analysis for disease duration.
>>>>>>> I've therefore generated a second qdec.table.dat file inserting the
>>>>>>> disease duration column with the following structure:
>>>>>>> fsid group duration
>>>>>>> Input subj1 1 13
>>>>>>> Input subj2 0
>>>>>>>
>>>>>>> (For healthy controls group (group 0) I've tried both options, leaving
>>>>>>> the duration column blank or inserting 0 as a value).
>>>>>>> I've also left the group.level file the same of the previous analysis.
>>>>>>> However, when i open the new qdec.table.dat file with qdec I get
>>>>>>> problems in correctly uploading the data.
>>>>>>> In particular, I get the following error:
>>>>>>>
>>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>>>>>>> Possible problem with experimental design:
>>>>>>> Check for duplicate entries and/or lack of range of continuous
>>>>>>> variables within a class.
>>>>>>> If you seek help with this problem, make sure to send:
>>>>>>> ?This is the command line:
>>>>>>> ?mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh
>>>>>>> --fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods
>>>>>>> --glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage
>>>>>>> lh --label
>>>>>>> /home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C
>>>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
>>>>>>> --C
>>>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat
>>>>>>>
>>>>>>> Of course there is no range for the continuous variable (disease
>>>>>>> duration) in the control group, so I'm wondering how to overcome this
>>>>>>> and generate a?correct qdec.table.dat file.
>>>>>>>
>>>>>>> Thanks in advance for any help!
>>>>>>>
>>>>>>> Pilar
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 7
>>>>>> Date: Mon, 18 Nov 2019 18:30:46 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <ff691f12-1e79-1b2d-463b-3ae47ace83c2@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> I don't understand what you are trying to do. I'm very confused by your
>>>>>> mentioning of bert. What does bert have to do with any of your data?
>>>>>>
>>>>>> On 11/14/19 10:47 AM, An wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Oops sorry for the mistakenly?reply. I will pay more attention in the
>>>>>>> future.
>>>>>>>
>>>>>>> Bert is the folder with the anatomical data. I tried the following
>>>>>>> steps with the 4D volume but failed. Then I checked the registration
>>>>>>> result after bbregister and found that the volume was not registered.
>>>>>>> After that I tried another 4D volume to do the steps and successfully
>>>>>>> got the sampled intensity onto the surface.
>>>>>>>
>>>>>>> The difference between the new 4D volume I used and the previous one
>>>>>>> is that there are two transformation matrices between them. The 4D
>>>>>>> dataset that I previously used but failed is the volume already
>>>>>>> registered to its anatomical volume(by using others tools). The new 4D
>>>>>>> volume that I tried and succeed is the volume not registered.
>>>>>>>
>>>>>>> I have no idea why the 4D volume after the transformation would cause
>>>>>>> a failed result. Could you please let me know that?
>>>>>>>
>>>>>>> Many thanks.
>>>>>>>
>>>>>>> Best,
>>>>>>> An
>>>>>>>
>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?13??? ??12:20???
>>>>>>>
>>>>>>>   If you have an anatomical MR that you have run through recon-all,
>>>>>>>   then
>>>>>>>   just use that one instead of bert in your steps below
>>>>>>>   ps. Please remember to post to the FS list and not to us personally
>>>>>>>
>>>>>>>   On 11/12/19 8:41 PM, an wrote:
>>>>>>>> ????????External Email - Use Caution
>>>>>>>>
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> I got the 4D fMRI dataset from others and it is not raw data. In
>>>>>>>   order
>>>>>>>> to run mri_vol2surf, I need to calculate the register.dat for the
>>>>>>>> required flag --srcreg so I tried in this way.
>>>>>>>>
>>>>>>>> FYI, the 4D fMRI dataset should have been registered with its
>>>>>>>> anatomical MR volume by using other tools.
>>>>>>>>
>>>>>>>> For now I only ran the recon-all on its anatomical MR volume
>>>>>>>   without
>>>>>>>> running the functional stream as I don't have the raw data.
>>>>>>>>
>>>>>>>> Should I also run the raw fMRI data from scratch by using
>>>>>>>   functional
>>>>>>>> stream? Or if I can run mri_vol2surf independently, which command
>>>>>>>> should I use to get a register.dat file?
>>>>>>>> In addition, the intensity of the 4D fMRI dataset I have is between
>>>>>>>> [-1, 1] and not integers, would this cause any problem?
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>>
>>>>>>>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>>> Don't do the 1st step.
>>>>>>>>> Why are you registering it to bert? I'm pretty sure bert did not
>>>>>>>>> participate in your fmri study
>>>>>>>>> When you run mri_vol2surf, it will probably work better with
>>>>>>>>> --projfrac 0.5
>>>>>>>>>
>>>>>>>>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>>>> ????????External Email - Use Caution
>>>>>>>>>>
>>>>>>>>>> Hi Prof. Greve,
>>>>>>>>>>
>>>>>>>>>> Thanks for your reply and sorry for the confusion.
>>>>>>>>>>
>>>>>>>>>> I have a 4D fMRI dataset with 10 time frames, where the
>>>>>>>   intensity of
>>>>>>>>>> each voxel is between [-1,1] and not integers. I want to map the
>>>>>>>>>> intensities of the volumes on its corresponding surface in
>>>>>>>   order to
>>>>>>>>>> get the functional values on each vertex in each frame. I have
>>>>>>>>>> already run its corresponding anatomical image in freesurfer.
>>>>>>>>>>
>>>>>>>>>> To achieve it, I tried the following steps:
>>>>>>>>>> 1. conform the fmri series by using mri_convert
>>>>>>>>>> 2. register the fmri series with the anatomy image by using
>>>>>>>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg
>>>>>>>   register.dat
>>>>>>>>>> 3. assign values from volumes to each vertex by using
>>>>>>>   mri_vol2surf:
>>>>>>>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg
>>>>>>>>>> register.dat --hemi lh
>>>>>>>>>> ? ? I also tried the -regheader in mri_vol2surf: mri_vol2surf
>>>>>>>   --src
>>>>>>>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>   freeview. But
>>>>>>>>>> after step2, the registered volume looks wrong. I am wondering
>>>>>>>   could
>>>>>>>>>> I use bbregister to register multi-frame fMRI series to a single
>>>>>>>>>> volume?
>>>>>>>>>> I also tried to use --regheader to replace the --srcreg file in
>>>>>>>>>> mri_vol2surf as the output register.dat in step2 is wrong. But
>>>>>>>   the
>>>>>>>>>> output is still wrong.
>>>>>>>>>>
>>>>>>>>>> Many thanks.
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>> An
>>>>>>>>>>
>>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>>> ?2019?11?11??? ??12:16???
>>>>>>>>>> ? ? ?When you say it is 4D, what do you mean? That each label
>>>>>>>   has its
>>>>>>>>>> ? ? ?own frame?
>>>>>>>>>>
>>>>>>>>>> ? ? ?On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> ????????External Email - Use Caution
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> Hi there,
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> I am working with creating a surface parcellation from a
>>>>>>>>>> ? ? ?volumetric
>>>>>>>>>> ? ? ?> parcellation and have some questions as follows:
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> 1. If the volumetric parcellation is a labeled 4D
>>>>>>>   multi-frame
>>>>>>>>>> ? ? ?dataset,
>>>>>>>>>> ? ? ?> could I still use the mris_sample_parc? Or could
>>>>>>>   mri_vol2surf
>>>>>>>>>> ? ? ?get the
>>>>>>>>>> ? ? ?> sampled labels for every vertex?
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> 2. For the 4D multi-frame dataset and mri_vol2surf output
>>>>>>>>>> ? ? ?results,
>>>>>>>>>> ? ? ?> which GUI should I use to visualize it? I tried freeview
>>>>>>>   for 4D
>>>>>>>>>> ? ? ?> multi-frame dataset but it looks weird.
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> 3. Is there any command to separate?multi-frame volume to
>>>>>>>>>> ? ? ?single frame
>>>>>>>>>> ? ? ?> volumes?
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> Many thanks!
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> Best,
>>>>>>>>>> ? ? ?> An
>>>>>>>>>> ? ? ?>
>>>>>>>>>> ? ? ?> _______________________________________________
>>>>>>>>>> ? ? ?> Freesurfer mailing list
>>>>>>>>>> ? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>> ? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ?_______________________________________________
>>>>>>>>>> ? ? ?Freesurfer mailing list
>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>> _______________________________________________
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>>   The information in this e-mail is intended only for the person to
>>>>>>>   whom it is
>>>>>>>   addressed. If you believe this e-mail was sent to you in error and
>>>>>>>   the e-mail
>>>>>>>   contains patient information, please contact the Partners
>>>>>>>   Compliance HelpLine at
>>>>>>>   http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>>>   you in error
>>>>>>>   but does not contain patient information, please contact the
>>>>>>>   sender and properly
>>>>>>>   dispose of the e-mail.
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 8
>>>>>> Date: Mon, 18 Nov 2019 18:31:35 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] Multiple comparisons
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <745185b7-5ebb-43bf-6d2d-b7328622fe5f@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> My preferred method is to use permutation
>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>>>>>>
>>>>>> On 11/14/19 12:29 PM, Juan Rivas wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> I would like to know how the correction is made for multiple
>>>>>>> comparisons in the statistical analysis? We are using QDEC, with False
>>>>>>> Discovery Rate or Montecarlo Null-Z. Is there a better way to do that?
>>>>>>> Best,
>>>>>>> JC.
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 9
>>>>>> Date: Mon, 18 Nov 2019 18:38:43 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] Questions for PetSurfer
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <f98e29f6-3532-91ed-021f-1e947468f57f@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 11/15/19 4:19 AM, Soo-Jong Kim wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Dear FreeSurfer experts,
>>>>>>>
>>>>>>> I am a student in neuroimaging using FreeSurfer.
>>>>>>> I have some questions and I don't know where to send questions.
>>>>>>> That's why I found this mail and writing.
>>>>>>>
>>>>>>> I've studied PetSurfer for partial volume correction of PET.
>>>>>>> I saw the tutorial in website.
>>>>>>> Originally, I want to use RBV method for pvcorrected PET for SUVR
>>>>>>> analysis.
>>>>>>>
>>>>>>> After generating gtmseg and coregistration to make lta file, I
>>>>>>> followed this code and changed some.
>>>>>>>
>>>>>>> *mri_gtmpvc --i PET.nii --reg subj1.reg.lta --psf 5 --seg gtmseg.mgz *
>>>>>>> *--default-seg-merge --auto-mask PSF .01 --no-rescale --no-reduce-fov
>>>>>>> --rbv --o output_pvc*
>>>>>>>
>>>>>>> After this, rbv.nii.gz file was generated. and SUVR analysis was
>>>>>>> performed as reference region (cerebellar cortex).? But Compared to
>>>>>>> original un-pvc PET, Cortex SUVR was reduced...
>>>>>>>
>>>>>>> In ideal pv-corrected PET, cortex SUVR was higher than?un-pvc PET.
>>>>>>>
>>>>>>> Is is okay if I use the output file as rbv.nii.gz ?
>>>>>> Yes, it does work. Is your tracer one where you expect GM > WM?
>>>>>>> in Thomas et al, 2011,
>>>>>>> He used aparc+aseg.mgz file from FreeSurfer. and he merged some regions.
>>>>>>> Frontal, Temporal, Occipital and so on. (Only gray matter to correct
>>>>>>> PET using RBV method)
>>>>>>>
>>>>>>> In that case, What are the regions to make rbv.nii.gz method in PetSurfer?
>>>>>> Look in aux/seg.ctab (you can visualize the aux/seg.nii.gz)
>>>>>>> Can I use the rbv.nii.gz as partial volume corrected PET from RBV method?
>>>>>> Yes
>>>>>>> If not, Please tell me what is the correct command of mri_gtmpvc.
>>>>>>> I need only partial volume corrected PET using RBV method.
>>>>>>>
>>>>>>> Sincerely,
>>>>>>>
>>>>>>> Soo-Jong Kim
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 10
>>>>>> Date: Mon, 18 Nov 2019 18:39:32 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] Cortical thickness values on a vertex base
>>>>>>   level
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <b9a9830f-fe4d-0321-ede7-1e0a3ee82ca0@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="Windows-1252"
>>>>>>
>>>>>> The sig file
>>>>>>
>>>>>> On 11/15/19 9:16 AM, Aicha Dijkshoorn wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Thank you so much for your repsonse.
>>>>>>> Could you maybe please tell us which input file we should use?
>>>>>>>
>>>>>>> Best wishes,
>>>>>>> AIcha
>>>>>>> ------------------------------------------------------------------------
>>>>>>> *Van:* freesurfer-bounces@nmr.mgh.harvard.edu
>>>>>>> <freesurfer-bounces@nmr.mgh.harvard.edu> namens Greve, Douglas
>>>>>>> N.,Ph.D. <DGREVE@mgh.harvard.edu>
>>>>>>> *Verzonden:* donderdag 31 oktober 2019 19:16
>>>>>>> *Aan:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
>>>>>>> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex
>>>>>>> base level
>>>>>>> You can run mri_surfcluster with your fdr threshold as the --thmin
>>>>>>> value. This will output cluster number (ocn) map. This will assign the
>>>>>>> cluster number to a vertex. You can then use mri_segstats with --seg
>>>>>>> ocn.mgz --excludeid 0 and input being the mean thickness or area maps.
>>>>>>> When you use area as thhe input, make sure to --accumulate to get the
>>>>>>> total area. You can get an area map in the same way that you got the
>>>>>>> thickness map, ie, mris_preproc, etc
>>>>>>>
>>>>>>> On 10/31/19 1:28 PM, Aicha Dijkshoorn wrote:
>>>>>>>> ????????External Email - Use Caution
>>>>>>>>
>>>>>>>> Dear Greve,
>>>>>>>>
>>>>>>>> Thank you for your quick respons.
>>>>>>>>
>>>>>>>> Yes, I believe that is what I mean. Let me illustrate with some
>>>>>>>> (fictive) data;
>>>>>>>> We were able to prove these data for the entire hemisphere as can be
>>>>>>>> seen below.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> *Group 1*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> *Group 2*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> *Difference*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> */Sig./*
>>>>>>>>
>>>>>>>> Thickness
>>>>>>>>
>>>>>>>> (in mm)
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Left
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 1.48
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 1.46
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> .004
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> .19
>>>>>>>>
>>>>>>>> Right
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 1.46
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 1.46
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> .003
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> .03
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> However, we would like to provide similar data in our vertex-base
>>>>>>>> analyses:
>>>>>>>>
>>>>>>>> *Significantly different clusters between group 1 and group 2*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> *Cortical thickness group 1*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> *Cortical thickness group 2*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> *Difference in mm2*
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> */Sig./*
>>>>>>>>
>>>>>>>> Left Cuneus
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 0.013
>>>>>>>>
>>>>>>>> Left Fusiform gyrus
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 0.021
>>>>>>>>
>>>>>>>> Right Paracentral lobule
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 0.001
>>>>>>>>
>>>>>>>> Right parahippocampal gyrus
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 0.002
>>>>>>>>
>>>>>>>>
>>>>>>>> Does this clarify my question?
>>>>>>>>
>>>>>>>> Best wishes,
>>>>>>>> Aicha
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> *Van:* freesurfer-bounces@nmr.mgh.harvard.edu
>>>>>>>> <freesurfer-bounces@nmr.mgh.harvard.edu> namens Greve, Douglas
>>>>>>>> N.,Ph.D. <DGREVE@mgh.harvard.edu>
>>>>>>>> *Verzonden:* donderdag 31 oktober 2019 16:25
>>>>>>>> *Aan:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex
>>>>>>>> base level
>>>>>>>> I'm not sure what you mean. Do you want the mean thickness of a cluster
>>>>>>>> and/or its surface area?
>>>>>>>>
>>>>>>>> On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
>>>>>>>>> ????????External Email - Use Caution
>>>>>>>>>
>>>>>>>>> Dear developers,
>>>>>>>>>
>>>>>>>>> For a case-control study we are comparing the cortical thickness and
>>>>>>>>> cortical surface area on a vertex-base level, for which we found
>>>>>>>>> significant differences throughout the brain.
>>>>>>>>>
>>>>>>>>> Is it possible that, in addition to the significance values (p < .05
>>>>>>>>> after FDR correction) on a vertex-base level, we can include the exact
>>>>>>>>> thickness or surface area value (or difference) of the significant
>>>>>>>>> clusters on a vertex base-level between the groups. In order words, to
>>>>>>>>> provide some measures to highlight the size of the significant cluster
>>>>>>>>> or the differences in cortical thickness / cortical surface area to
>>>>>>>>> provide clinically useful context. For instance, a command comparable
>>>>>>>>> to 'voxel size' in TBSS.
>>>>>>>>>
>>>>>>>>> As this is my first time using Freesurfer any help that you could
>>>>>>>>> offer on this matter would be highly appreciated.
>>>>>>>>>
>>>>>>>>> Best wishes,
>>>>>>>>> Brigitte Dijkshoorn
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 11
>>>>>> Date: Mon, 18 Nov 2019 18:41:37 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] Question about the input for longitudinal
>>>>>>   processing pipeline
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <d5205fe6-329a-f9b4-252a-8f1857aa42e4@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> Do all images and time points have contrast? If some do and some don't,
>>>>>> then I don't think you can properly do the analysis?
>>>>>>
>>>>>> On 11/15/19 10:06 AM, Darko Komneni? wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Dear Freesurfer experts,
>>>>>>> I wanted to run the Freesurfer's longitudinal processing pipeline
>>>>>>> (described here
>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) on a
>>>>>>> series of MRI scans from a single patient. However, after looking at
>>>>>>> the scans, i realized that for most time points, the patient doesn't
>>>>>>> have a "simple/normal" T1 MPRAGE sequence available. Instead, they
>>>>>>> have a T1 sequence with a contrast agent, as well as T1 mp2rage
>>>>>>> sequences.
>>>>>>>
>>>>>>> Is it possible/advisable to run recon-all in general or this pipeline
>>>>>>> in particular on T1 MPRAGE scans that have a contrast agent, or that
>>>>>>> are mp2rage instead of MPRAGE?
>>>>>>>
>>>>>>> Thanks in advance!
>>>>>>> Best,
>>>>>>> Darko
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 12
>>>>>> Date: Mon, 18 Nov 2019 18:45:17 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] Brain lobules pooling- request
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <a457c4e8-913e-706e-c7ef-8925c7eaad3d@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="Windows-1252"
>>>>>>
>>>>>> sorry, it is not clear to me what is going wrong here. Did the
>>>>>> mri_annotation2label command fail? or mris_anatomical_stats command?
>>>>>>
>>>>>> On 11/17/19 9:55 PM, Samson Nivins wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Hi FreeSurfer Team,
>>>>>>>
>>>>>>> ????? I am interested in individual lobular volume and thickness. So I
>>>>>>> have extracted based on the Q and A I created few script to run and
>>>>>>> extract the data.
>>>>>>>
>>>>>>> However, I got few questions regarding thickness and WM
>>>>>>>
>>>>>>> For extracting lobular GM I used
>>>>>>>
>>>>>>> mri_annotation2label --subject 1014? --hemi lh --lobesStrict
>>>>>>> lh.lobesStrict.annot
>>>>>>>
>>>>>>> mri_annotation2label --subject 1014? --hemi lh --annotation
>>>>>>> lobesStrict --outdir
>>>>>>> '/home/samson/Volume/freesurfer/subjects/recon-all_working/lh'
>>>>>>>
>>>>>>> for computing stats I used
>>>>>>>
>>>>>>> mris_anatomical_stats -l
>>>>>>> '/home/samson/Volume/freesurfer/subjects/recon-all_working/lh/lh.occipital.label'
>>>>>>> -b 1014 lh
>>>>>>>
>>>>>>> I am not sure, whether any command is there to export the data.
>>>>>>>
>>>>>>> And, the average cortical thickness which we obtain in the terminal
>>>>>>> window during individual extraction, does it correspond to the lobular
>>>>>>> thickness or as whole
>>>>>>>
>>>>>>> For example
>>>>>>>
>>>>>>> I extracted stats for left frontal cortex:
>>>>>>>
>>>>>>> I got the following details in Terminal window
>>>>>>>
>>>>>>> Number of vertices, Total surface area, total gray matter, average
>>>>>>> cortical thickness ?.
>>>>>>>
>>>>>>> In this average cortical thickness ? correspond to the ROI specifc are
>>>>>>> as a whole?
>>>>>>>
>>>>>>> Thanks for you help.
>>>>>>>
>>>>>>> Looking forward to hearing from you
>>>>>>>
>>>>>>> Cheers
>>>>>>>
>>>>>>> Best regards,
>>>>>>>
>>>>>>> Sam
>>>>>>>
>>>>>>> *Samson Nivins? |**PhD Student*
>>>>>>>
>>>>>>> **
>>>>>>>
>>>>>>> *A*The University of Auckland, Liggins Institute
>>>>>>>
>>>>>>> Building 505, Level 2, 85 Park Road, Auckland
>>>>>>>
>>>>>>> *Ph *+(64) 21 256 5964
>>>>>>>
>>>>>>> *E*samson.nivins@gmail.com <mailto:samson.nivins@gmail.com>
>>>>>>>
>>>>>>> *//*
>>>>>>>
>>>>>>> cid:image001.png@01D4C1F6.9273DF90
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 13
>>>>>> Date: Mon, 18 Nov 2019 13:48:58 -0500
>>>>>> From: An <annaqu1024@gmail.com>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <CAJVCUNcDB0ggDRvgbBVYBzftLTdQ42jvUhGhO0+UKe+tkniRoA@mail.gmail.com>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>       External Email - Use Caution
>>>>>>
>>>>>> I want to map the intensities of the volumes on its corresponding surface
>>>>>> in order to get the functional values on each vertex in each frame. I ran
>>>>>> recon-all for the anatomical volume and saved all outputs(mri,labels,surf
>>>>>> and etc.) in the bert folder. I use it because I need to specify the
>>>>>> required flag -s in bbregister in order to register the functional volume
>>>>>> to its anatomical volume.
>>>>>>
>>>>>> Many thanks.
>>>>>>
>>>>>> Best,
>>>>>> An
>>>>>>
>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> ?2019?11?18??? ??1:31???
>>>>>>
>>>>>>> I don't understand what you are trying to do. I'm very confused by your
>>>>>>> mentioning of bert. What does bert have to do with any of your data?
>>>>>>>
>>>>>>> On 11/14/19 10:47 AM, An wrote:
>>>>>>>>       External Email - Use Caution
>>>>>>>>
>>>>>>>> Oops sorry for the mistakenly reply. I will pay more attention in the
>>>>>>>> future.
>>>>>>>>
>>>>>>>> Bert is the folder with the anatomical data. I tried the following
>>>>>>>> steps with the 4D volume but failed. Then I checked the registration
>>>>>>>> result after bbregister and found that the volume was not registered.
>>>>>>>> After that I tried another 4D volume to do the steps and successfully
>>>>>>>> got the sampled intensity onto the surface.
>>>>>>>>
>>>>>>>> The difference between the new 4D volume I used and the previous one
>>>>>>>> is that there are two transformation matrices between them. The 4D
>>>>>>>> dataset that I previously used but failed is the volume already
>>>>>>>> registered to its anatomical volume(by using others tools). The new 4D
>>>>>>>> volume that I tried and succeed is the volume not registered.
>>>>>>>>
>>>>>>>> I have no idea why the 4D volume after the transformation would cause
>>>>>>>> a failed result. Could you please let me know that?
>>>>>>>>
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?13??? ??12:20???
>>>>>>>>
>>>>>>>>   If you have an anatomical MR that you have run through recon-all,
>>>>>>>>   then
>>>>>>>>   just use that one instead of bert in your steps below
>>>>>>>>   ps. Please remember to post to the FS list and not to us personally
>>>>>>>>
>>>>>>>>   On 11/12/19 8:41 PM, an wrote:
>>>>>>>>>       External Email - Use Caution
>>>>>>>>>
>>>>>>>>> Many thanks.
>>>>>>>>>
>>>>>>>>> I got the 4D fMRI dataset from others and it is not raw data. In
>>>>>>>>   order
>>>>>>>>> to run mri_vol2surf, I need to calculate the register.dat for the
>>>>>>>>> required flag --srcreg so I tried in this way.
>>>>>>>>>
>>>>>>>>> FYI, the 4D fMRI dataset should have been registered with its
>>>>>>>>> anatomical MR volume by using other tools.
>>>>>>>>>
>>>>>>>>> For now I only ran the recon-all on its anatomical MR volume
>>>>>>>>   without
>>>>>>>>> running the functional stream as I don't have the raw data.
>>>>>>>>>
>>>>>>>>> Should I also run the raw fMRI data from scratch by using
>>>>>>>>   functional
>>>>>>>>> stream? Or if I can run mri_vol2surf independently, which command
>>>>>>>>> should I use to get a register.dat file?
>>>>>>>>> In addition, the intensity of the 4D fMRI dataset I have is between
>>>>>>>>> [-1, 1] and not integers, would this cause any problem?
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> An
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>>>> Don't do the 1st step.
>>>>>>>>>> Why are you registering it to bert? I'm pretty sure bert did not
>>>>>>>>>> participate in your fmri study
>>>>>>>>>> When you run mri_vol2surf, it will probably work better with
>>>>>>>>>> --projfrac 0.5
>>>>>>>>>>
>>>>>>>>>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>>>>>       External Email - Use Caution
>>>>>>>>>>>
>>>>>>>>>>> Hi Prof. Greve,
>>>>>>>>>>>
>>>>>>>>>>> Thanks for your reply and sorry for the confusion.
>>>>>>>>>>>
>>>>>>>>>>> I have a 4D fMRI dataset with 10 time frames, where the
>>>>>>>>   intensity of
>>>>>>>>>>> each voxel is between [-1,1] and not integers. I want to map the
>>>>>>>>>>> intensities of the volumes on its corresponding surface in
>>>>>>>>   order to
>>>>>>>>>>> get the functional values on each vertex in each frame. I have
>>>>>>>>>>> already run its corresponding anatomical image in freesurfer.
>>>>>>>>>>>
>>>>>>>>>>> To achieve it, I tried the following steps:
>>>>>>>>>>> 1. conform the fmri series by using mri_convert
>>>>>>>>>>> 2. register the fmri series with the anatomy image by using
>>>>>>>>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg
>>>>>>>>   register.dat
>>>>>>>>>>> 3. assign values from volumes to each vertex by using
>>>>>>>>   mri_vol2surf:
>>>>>>>>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg
>>>>>>>>>>> register.dat --hemi lh
>>>>>>>>>>>   I also tried the -regheader in mri_vol2surf: mri_vol2surf
>>>>>>>>   --src
>>>>>>>>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>>   freeview. But
>>>>>>>>>>> after step2, the registered volume looks wrong. I am wondering
>>>>>>>>   could
>>>>>>>>>>> I use bbregister to register multi-frame fMRI series to a single
>>>>>>>>>>> volume?
>>>>>>>>>>> I also tried to use --regheader to replace the --srcreg file in
>>>>>>>>>>> mri_vol2surf as the output register.dat in step2 is wrong. But
>>>>>>>>   the
>>>>>>>>>>> output is still wrong.
>>>>>>>>>>>
>>>>>>>>>>> Many thanks.
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>> An
>>>>>>>>>>>
>>>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>>> ?2019?11?11??? ??12:16???
>>>>>>>>>>>   When you say it is 4D, what do you mean? That each label
>>>>>>>>   has its
>>>>>>>>>>>   own frame?
>>>>>>>>>>>
>>>>>>>>>>>   On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>>>>>>       External Email - Use Caution
>>>>>>>>>>>>
>>>>>>>>>>>> Hi there,
>>>>>>>>>>>>
>>>>>>>>>>>> I am working with creating a surface parcellation from a
>>>>>>>>>>>   volumetric
>>>>>>>>>>>> parcellation and have some questions as follows:
>>>>>>>>>>>>
>>>>>>>>>>>> 1. If the volumetric parcellation is a labeled 4D
>>>>>>>>   multi-frame
>>>>>>>>>>>   dataset,
>>>>>>>>>>>> could I still use the mris_sample_parc? Or could
>>>>>>>>   mri_vol2surf
>>>>>>>>>>>   get the
>>>>>>>>>>>> sampled labels for every vertex?
>>>>>>>>>>>>
>>>>>>>>>>>> 2. For the 4D multi-frame dataset and mri_vol2surf output
>>>>>>>>>>>   results,
>>>>>>>>>>>> which GUI should I use to visualize it? I tried freeview
>>>>>>>>   for 4D
>>>>>>>>>>>> multi-frame dataset but it looks weird.
>>>>>>>>>>>>
>>>>>>>>>>>> 3. Is there any command to separate multi-frame volume to
>>>>>>>>>>>   single frame
>>>>>>>>>>>> volumes?
>>>>>>>>>>>>
>>>>>>>>>>>> Many thanks!
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Best,
>>>>>>>>>>>> An
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>   Freesurfer mailing list
>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>   The information in this e-mail is intended only for the person to
>>>>>>>>   whom it is
>>>>>>>>   addressed. If you believe this e-mail was sent to you in error and
>>>>>>>>   the e-mail
>>>>>>>>   contains patient information, please contact the Partners
>>>>>>>>   Compliance HelpLine at
>>>>>>>>   http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>>>>   you in error
>>>>>>>>   but does not contain patient information, please contact the
>>>>>>>>   sender and properly
>>>>>>>>   dispose of the e-mail.
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> -------------- next part --------------
>>>>>> An HTML attachment was scrubbed...
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>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 14
>>>>>> Date: Mon, 18 Nov 2019 19:27:31 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] (no subject)
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <bc2fb054-9b5d-938d-a2ea-5fafb4a27d5c@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> It gets the subcortical from apas+head.mgz which gets created along the
>>>>>> way by xcerebralseg. You can create your own with xcerebralseg by
>>>>>> specifying your volume as the mergevol. I think this will work, but I'm
>>>>>> not sure. I'm assuming you've used the GCA to create your own
>>>>>> subcortical seg for the given subject
>>>>>>
>>>>>> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> I just realized that the above?mentioned command (gtmseg --s XYZ --o
>>>>>>> BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
>>>>>>> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg)
>>>>>>> gives me only the cortical segmentation. Is there any way to also
>>>>>>> include the subcortical segmentation based on my individual atlas? I
>>>>>>> also have an Atlas_subcortex.gca file available.
>>>>>>>
>>>>>>> Best,
>>>>>>> Boris
>>>>>>>
>>>>>>> On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
>>>>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
>>>>>>>
>>>>>>>   There is no cut off for the minimum size. As it gets smaller, the PVC
>>>>>>>   noise amplification will become bigger (it also depends on the
>>>>>>>   shape as
>>>>>>>   well).
>>>>>>>
>>>>>>>   I think the --no-xcerseg is the right way to go now
>>>>>>>
>>>>>>>   On 8/13/19 11:00 AM, Boris Rauchmann wrote:
>>>>>>>> ????????External Email - Use Caution
>>>>>>>>
>>>>>>>> Thank you for your prompt answer - the command worked. This is the
>>>>>>>> atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
>>>>>>>> What is approximately the smallest possible segment when using PVC?
>>>>>>>> Also, does the exclusion of extracerebral structures harm? I
>>>>>>>   used that
>>>>>>>> flag because it complained:
>>>>>>>>
>>>>>>>> gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
>>>>>>>> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
>>>>>>>> ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
>>>>>>>> but you must indicate whether to use what is there (--no-xcerseg)
>>>>>>>> or create a new one and overwrite what is there (--xcerseg)
>>>>>>>> or specify your own headseg (--head)
>>>>>>>>
>>>>>>>> and did not want to override my apas+head.mgz
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Boris
>>>>>>>>
>>>>>>>> On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
>>>>>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>   wrote:
>>>>>>>> ? ? ?I don't know what the Brainnetome is, but it looks like you have
>>>>>>>> ? ? ?it in
>>>>>>>> ? ? ?annotation form. I think that command should work. Why are
>>>>>>>   you using
>>>>>>>> ? ? ?--no-xcerseg? This will cause it to not include extracerebral
>>>>>>>> ? ? ?structures. Also note that you cannot use arbitrarily small
>>>>>>>   segments
>>>>>>>> ? ? ?when doing PVC.
>>>>>>>>
>>>>>>>> ? ? ?On 8/13/19 10:26 AM, Boris Rauchmann wrote:
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Dear all,
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> my intention is to use the Brainnetome Atlas
>>>>>>>> ? ? ?parcellation/segmentation
>>>>>>>> ? ? ?> in PETSurfer to obtain PVC corrected SUVRs for the atlas
>>>>>>>   ROIs. I
>>>>>>>> ? ? ?used:
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot
>>>>>>>   BN_Atlas.annot --ctab
>>>>>>>> ? ? ?> '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
>>>>>>>   --no-xcerseg
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Is this the right approach to obtain a high resolution
>>>>>>>> ? ? ?segmentation to
>>>>>>>> ? ? ?> run PVC methods?
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Thanks,
>>>>>>>> ? ? ?> Boris
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> _______________________________________________
>>>>>>>> ? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> ? ? ?_______________________________________________
>>>>>>>> ? ? ?Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>   _______________________________________________
>>>>>>>   Freesurfer mailing list
>>>>>>>   Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 15
>>>>>> Date: Mon, 18 Nov 2019 19:32:49 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <7d550731-08c1-d66c-5dca-d14bb313ba5c@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> What was your original recon-all command?
>>>>>>
>>>>>> On 11/18/19 1:48 PM, An wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> I want to map the intensities of the volumes on its corresponding
>>>>>>> surface in order to get the functional values on each vertex in each
>>>>>>> frame.?I ran recon-all for the anatomical volume and saved all
>>>>>>> outputs(mri,labels,surf and etc.) in the bert folder. I use it because
>>>>>>> I need to specify?the required flag -s in bbregister in order to
>>>>>>> register the functional volume to its anatomical volume.
>>>>>>>
>>>>>>> Many thanks.
>>>>>>>
>>>>>>> Best,
>>>>>>> An
>>>>>>>
>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?18??? ??1:31???
>>>>>>>
>>>>>>>   I don't understand what you are trying to do. I'm very confused by
>>>>>>>   your
>>>>>>>   mentioning of bert. What does bert have to do with any of your data?
>>>>>>>
>>>>>>>   On 11/14/19 10:47 AM, An wrote:
>>>>>>>> ????????External Email - Use Caution
>>>>>>>>
>>>>>>>> Oops sorry for the mistakenly?reply. I will pay more attention
>>>>>>>   in the
>>>>>>>> future.
>>>>>>>>
>>>>>>>> Bert is the folder with the anatomical data. I tried the following
>>>>>>>> steps with the 4D volume but failed. Then I checked the
>>>>>>>   registration
>>>>>>>> result after bbregister and found that the volume was not
>>>>>>>   registered.
>>>>>>>> After that I tried another 4D volume to do the steps and
>>>>>>>   successfully
>>>>>>>> got the sampled intensity onto the surface.
>>>>>>>>
>>>>>>>> The difference between the new 4D volume I used and the previous
>>>>>>>   one
>>>>>>>> is that there are two transformation matrices between them. The 4D
>>>>>>>> dataset that I previously used but failed is the volume already
>>>>>>>> registered to its anatomical volume(by using others tools). The
>>>>>>>   new 4D
>>>>>>>> volume that I tried and succeed is the volume not registered.
>>>>>>>>
>>>>>>>> I have no idea why the 4D volume after the transformation would
>>>>>>>   cause
>>>>>>>> a failed result. Could you please let me know that?
>>>>>>>>
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>   ?2019?11?13??? ??12:20???
>>>>>>>> ? ? ?If you have an anatomical MR that you have run through
>>>>>>>   recon-all,
>>>>>>>> ? ? ?then
>>>>>>>> ? ? ?just use that one instead of bert in your steps below
>>>>>>>> ? ? ?ps. Please remember to post to the FS list and not to us
>>>>>>>   personally
>>>>>>>> ? ? ?On 11/12/19 8:41 PM, an wrote:
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Many thanks.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> I got the 4D fMRI dataset from others and it is not raw
>>>>>>>   data. In
>>>>>>>> ? ? ?order
>>>>>>>> ? ? ?> to run mri_vol2surf, I need to calculate the register.dat
>>>>>>>   for the
>>>>>>>> ? ? ?> required flag --srcreg so I tried in this way.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> FYI, the 4D fMRI dataset should have been registered with its
>>>>>>>> ? ? ?> anatomical MR volume by using other tools.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> For now I only ran the recon-all on its anatomical MR volume
>>>>>>>> ? ? ?without
>>>>>>>> ? ? ?> running the functional stream as I don't have the raw data.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Should I also run the raw fMRI data from scratch by using
>>>>>>>> ? ? ?functional
>>>>>>>> ? ? ?> stream? Or if I can run mri_vol2surf independently, which
>>>>>>>   command
>>>>>>>> ? ? ?> should I use to get a register.dat file?
>>>>>>>> ? ? ?> In addition, the intensity of the 4D fMRI dataset I have
>>>>>>>   is between
>>>>>>>> ? ? ?> [-1, 1] and not integers, would this cause any problem?
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Best,
>>>>>>>> ? ? ?> An
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>> ? ? ?>> Don't do the 1st step.
>>>>>>>> ? ? ?>> Why are you registering it to bert? I'm pretty sure bert
>>>>>>>   did not
>>>>>>>> ? ? ?>> participate in your fmri study
>>>>>>>> ? ? ?>> When you run mri_vol2surf, it will probably work better with
>>>>>>>> ? ? ?>> --projfrac 0.5
>>>>>>>> ? ? ?>>
>>>>>>>> ? ? ?>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> ????????External Email - Use Caution
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> Hi Prof. Greve,
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> Thanks for your reply and sorry for the confusion.
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> I have a 4D fMRI dataset with 10 time frames, where the
>>>>>>>> ? ? ?intensity of
>>>>>>>> ? ? ?>>> each voxel is between [-1,1] and not integers. I want to
>>>>>>>   map the
>>>>>>>> ? ? ?>>> intensities of the volumes on its corresponding surface in
>>>>>>>> ? ? ?order to
>>>>>>>> ? ? ?>>> get the functional values on each vertex in each frame.
>>>>>>>   I have
>>>>>>>> ? ? ?>>> already run its corresponding anatomical image in
>>>>>>>   freesurfer.
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> To achieve it, I tried the following steps:
>>>>>>>> ? ? ?>>> 1. conform the fmri series by using mri_convert
>>>>>>>> ? ? ?>>> 2. register the fmri series with the anatomy image by using
>>>>>>>> ? ? ?>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg
>>>>>>>> ? ? ?register.dat
>>>>>>>> ? ? ?>>> 3. assign values from volumes to each vertex by using
>>>>>>>> ? ? ?mri_vol2surf:
>>>>>>>> ? ? ?>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg
>>>>>>>> ? ? ?>>> register.dat --hemi lh
>>>>>>>> ? ? ?>>> ? ? I also tried the -regheader in mri_vol2surf:
>>>>>>>   mri_vol2surf
>>>>>>>> ? ? ?--src
>>>>>>>> ? ? ?>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>> ? ? ?freeview. But
>>>>>>>> ? ? ?>>> after step2, the registered volume looks wrong. I am
>>>>>>>   wondering
>>>>>>>> ? ? ?could
>>>>>>>> ? ? ?>>> I use bbregister to register multi-frame fMRI series to
>>>>>>>   a single
>>>>>>>> ? ? ?>>> volume?
>>>>>>>> ? ? ?>>> I also tried to use --regheader to replace the --srcreg
>>>>>>>   file in
>>>>>>>> ? ? ?>>> mri_vol2surf as the output register.dat in step2 is
>>>>>>>   wrong. But
>>>>>>>> ? ? ?the
>>>>>>>> ? ? ?>>> output is still wrong.
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> Many thanks.
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> Best,
>>>>>>>> ? ? ?>>> An
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>>>> ?2019?11?11???
>>>>>>>   ??12:16???
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>>? ? ?When you say it is 4D, what do you mean? That each label
>>>>>>>> ? ? ?has its
>>>>>>>> ? ? ?>>>? ? ?own frame?
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>>? ? ?On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> Hi there,
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> I am working with creating a surface parcellation
>>>>>>>   from a
>>>>>>>> ? ? ?>>>? ? ?volumetric
>>>>>>>> ? ? ?>>>? ? ?> parcellation and have some questions as follows:
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> 1. If the volumetric parcellation is a labeled 4D
>>>>>>>> ? ? ?multi-frame
>>>>>>>> ? ? ?>>>? ? ?dataset,
>>>>>>>> ? ? ?>>>? ? ?> could I still use the mris_sample_parc? Or could
>>>>>>>> ? ? ?mri_vol2surf
>>>>>>>> ? ? ?>>>? ? ?get the
>>>>>>>> ? ? ?>>>? ? ?> sampled labels for every vertex?
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> 2. For the 4D multi-frame dataset and mri_vol2surf
>>>>>>>   output
>>>>>>>> ? ? ?>>>? ? ?results,
>>>>>>>> ? ? ?>>>? ? ?> which GUI should I use to visualize it? I tried
>>>>>>>   freeview
>>>>>>>> ? ? ?for 4D
>>>>>>>> ? ? ?>>>? ? ?> multi-frame dataset but it looks weird.
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> 3. Is there any command to separate?multi-frame
>>>>>>>   volume to
>>>>>>>> ? ? ?>>>? ? ?single frame
>>>>>>>> ? ? ?>>>? ? ?> volumes?
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> Many thanks!
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> Best,
>>>>>>>> ? ? ?>>>? ? ?> An
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>>>? ? ?> _______________________________________________
>>>>>>>> ? ? ?>>>? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?>>>? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>>>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>>>? ? ?>
>>>>>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> ?_______________________________________________
>>>>>>>> ? ? ?>>>? ? ?Freesurfer mailing list
>>>>>>>> ? ? ?>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>>>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>>
>>>>>>>> ? ? ?>>> _______________________________________________
>>>>>>>> ? ? ?>>> Freesurfer mailing list
>>>>>>>> ? ? ?>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>>
>>>>>>>> ? ? ?>>
>>>>>>>> ? ? ?>> _______________________________________________
>>>>>>>> ? ? ?>> Freesurfer mailing list
>>>>>>>> ? ? ?>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ? ? ?The information in this e-mail is intended only for the
>>>>>>>   person to
>>>>>>>> ? ? ?whom it is
>>>>>>>> ? ? ?addressed. If you believe this e-mail was sent to you in
>>>>>>>   error and
>>>>>>>> ? ? ?the e-mail
>>>>>>>> ? ? ?contains patient information, please contact the Partners
>>>>>>>> ? ? ?Compliance HelpLine at
>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>>>> ? ? ?you in error
>>>>>>>> ? ? ?but does not contain patient information, please contact the
>>>>>>>> ? ? ?sender and properly
>>>>>>>> ? ? ?dispose of the e-mail.
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>   _______________________________________________
>>>>>>>   Freesurfer mailing list
>>>>>>>   Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 16
>>>>>> Date: Mon, 18 Nov 2019 14:53:24 -0500
>>>>>> From: An <annaqu1024@gmail.com>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <CAJVCUNfyc63KvvwVCuzw6EPVNVhbr0fSYs3m_2hP9-48OyA-ag@mail.gmail.com>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>       External Email - Use Caution
>>>>>>
>>>>>> Here is my recon-all command line:
>>>>>>
>>>>>> recon-all -i ana_Vol.nii -s bert -all
>>>>>>
>>>>>> Many thanks.
>>>>>>
>>>>>> Best,
>>>>>> An
>>>>>>
>>>>>>
>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> ?2019?11?18??? ??2:33???
>>>>>>
>>>>>>> What was your original recon-all command?
>>>>>>>
>>>>>>> On 11/18/19 1:48 PM, An wrote:
>>>>>>>>       External Email - Use Caution
>>>>>>>>
>>>>>>>> I want to map the intensities of the volumes on its corresponding
>>>>>>>> surface in order to get the functional values on each vertex in each
>>>>>>>> frame. I ran recon-all for the anatomical volume and saved all
>>>>>>>> outputs(mri,labels,surf and etc.) in the bert folder. I use it because
>>>>>>>> I need to specify the required flag -s in bbregister in order to
>>>>>>>> register the functional volume to its anatomical volume.
>>>>>>>>
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?18??? ??1:31???
>>>>>>>>
>>>>>>>>   I don't understand what you are trying to do. I'm very confused by
>>>>>>>>   your
>>>>>>>>   mentioning of bert. What does bert have to do with any of your data?
>>>>>>>>
>>>>>>>>   On 11/14/19 10:47 AM, An wrote:
>>>>>>>>>       External Email - Use Caution
>>>>>>>>>
>>>>>>>>> Oops sorry for the mistakenly reply. I will pay more attention
>>>>>>>>   in the
>>>>>>>>> future.
>>>>>>>>>
>>>>>>>>> Bert is the folder with the anatomical data. I tried the following
>>>>>>>>> steps with the 4D volume but failed. Then I checked the
>>>>>>>>   registration
>>>>>>>>> result after bbregister and found that the volume was not
>>>>>>>>   registered.
>>>>>>>>> After that I tried another 4D volume to do the steps and
>>>>>>>>   successfully
>>>>>>>>> got the sampled intensity onto the surface.
>>>>>>>>>
>>>>>>>>> The difference between the new 4D volume I used and the previous
>>>>>>>>   one
>>>>>>>>> is that there are two transformation matrices between them. The 4D
>>>>>>>>> dataset that I previously used but failed is the volume already
>>>>>>>>> registered to its anatomical volume(by using others tools). The
>>>>>>>>   new 4D
>>>>>>>>> volume that I tried and succeed is the volume not registered.
>>>>>>>>>
>>>>>>>>> I have no idea why the 4D volume after the transformation would
>>>>>>>>   cause
>>>>>>>>> a failed result. Could you please let me know that?
>>>>>>>>>
>>>>>>>>> Many thanks.
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> An
>>>>>>>>>
>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>>   ?2019?11?13??? ??12:20???
>>>>>>>>>   If you have an anatomical MR that you have run through
>>>>>>>>   recon-all,
>>>>>>>>>   then
>>>>>>>>>   just use that one instead of bert in your steps below
>>>>>>>>>   ps. Please remember to post to the FS list and not to us
>>>>>>>>   personally
>>>>>>>>>   On 11/12/19 8:41 PM, an wrote:
>>>>>>>>>>       External Email - Use Caution
>>>>>>>>>>
>>>>>>>>>> Many thanks.
>>>>>>>>>>
>>>>>>>>>> I got the 4D fMRI dataset from others and it is not raw
>>>>>>>>   data. In
>>>>>>>>>   order
>>>>>>>>>> to run mri_vol2surf, I need to calculate the register.dat
>>>>>>>>   for the
>>>>>>>>>> required flag --srcreg so I tried in this way.
>>>>>>>>>>
>>>>>>>>>> FYI, the 4D fMRI dataset should have been registered with its
>>>>>>>>>> anatomical MR volume by using other tools.
>>>>>>>>>>
>>>>>>>>>> For now I only ran the recon-all on its anatomical MR volume
>>>>>>>>>   without
>>>>>>>>>> running the functional stream as I don't have the raw data.
>>>>>>>>>>
>>>>>>>>>> Should I also run the raw fMRI data from scratch by using
>>>>>>>>>   functional
>>>>>>>>>> stream? Or if I can run mri_vol2surf independently, which
>>>>>>>>   command
>>>>>>>>>> should I use to get a register.dat file?
>>>>>>>>>> In addition, the intensity of the 4D fMRI dataset I have
>>>>>>>>   is between
>>>>>>>>>> [-1, 1] and not integers, would this cause any problem?
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>> An
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>>>>> Don't do the 1st step.
>>>>>>>>>>> Why are you registering it to bert? I'm pretty sure bert
>>>>>>>>   did not
>>>>>>>>>>> participate in your fmri study
>>>>>>>>>>> When you run mri_vol2surf, it will probably work better with
>>>>>>>>>>> --projfrac 0.5
>>>>>>>>>>>
>>>>>>>>>>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>>>>>>       External Email - Use Caution
>>>>>>>>>>>>
>>>>>>>>>>>> Hi Prof. Greve,
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks for your reply and sorry for the confusion.
>>>>>>>>>>>>
>>>>>>>>>>>> I have a 4D fMRI dataset with 10 time frames, where the
>>>>>>>>>   intensity of
>>>>>>>>>>>> each voxel is between [-1,1] and not integers. I want to
>>>>>>>>   map the
>>>>>>>>>>>> intensities of the volumes on its corresponding surface in
>>>>>>>>>   order to
>>>>>>>>>>>> get the functional values on each vertex in each frame.
>>>>>>>>   I have
>>>>>>>>>>>> already run its corresponding anatomical image in
>>>>>>>>   freesurfer.
>>>>>>>>>>>> To achieve it, I tried the following steps:
>>>>>>>>>>>> 1. conform the fmri series by using mri_convert
>>>>>>>>>>>> 2. register the fmri series with the anatomy image by using
>>>>>>>>>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg
>>>>>>>>>   register.dat
>>>>>>>>>>>> 3. assign values from volumes to each vertex by using
>>>>>>>>>   mri_vol2surf:
>>>>>>>>>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg
>>>>>>>>>>>> register.dat --hemi lh
>>>>>>>>>>>>   I also tried the -regheader in mri_vol2surf:
>>>>>>>>   mri_vol2surf
>>>>>>>>>   --src
>>>>>>>>>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>>>   freeview. But
>>>>>>>>>>>> after step2, the registered volume looks wrong. I am
>>>>>>>>   wondering
>>>>>>>>>   could
>>>>>>>>>>>> I use bbregister to register multi-frame fMRI series to
>>>>>>>>   a single
>>>>>>>>>>>> volume?
>>>>>>>>>>>> I also tried to use --regheader to replace the --srcreg
>>>>>>>>   file in
>>>>>>>>>>>> mri_vol2surf as the output register.dat in step2 is
>>>>>>>>   wrong. But
>>>>>>>>>   the
>>>>>>>>>>>> output is still wrong.
>>>>>>>>>>>>
>>>>>>>>>>>> Many thanks.
>>>>>>>>>>>>
>>>>>>>>>>>> Best,
>>>>>>>>>>>> An
>>>>>>>>>>>>
>>>>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>>
>>>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>>>> ?2019?11?11???
>>>>>>>>   ??12:16???
>>>>>>>>>>>>   When you say it is 4D, what do you mean? That each
>>>>>>> label
>>>>>>>>>   has its
>>>>>>>>>>>>   own frame?
>>>>>>>>>>>>
>>>>>>>>>>>>   On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>>>>>>>       External Email - Use Caution
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hi there,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I am working with creating a surface parcellation
>>>>>>>>   from a
>>>>>>>>>>>>   volumetric
>>>>>>>>>>>>> parcellation and have some questions as follows:
>>>>>>>>>>>>>
>>>>>>>>>>>>> 1. If the volumetric parcellation is a labeled 4D
>>>>>>>>>   multi-frame
>>>>>>>>>>>>   dataset,
>>>>>>>>>>>>> could I still use the mris_sample_parc? Or could
>>>>>>>>>   mri_vol2surf
>>>>>>>>>>>>   get the
>>>>>>>>>>>>> sampled labels for every vertex?
>>>>>>>>>>>>>
>>>>>>>>>>>>> 2. For the 4D multi-frame dataset and mri_vol2surf
>>>>>>>>   output
>>>>>>>>>>>>   results,
>>>>>>>>>>>>> which GUI should I use to visualize it? I tried
>>>>>>>>   freeview
>>>>>>>>>   for 4D
>>>>>>>>>>>>> multi-frame dataset but it looks weird.
>>>>>>>>>>>>>
>>>>>>>>>>>>> 3. Is there any command to separate multi-frame
>>>>>>>>   volume to
>>>>>>>>>>>>   single frame
>>>>>>>>>>>>> volumes?
>>>>>>>>>>>>>
>>>>>>>>>>>>> Many thanks!
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Best,
>>>>>>>>>>>>> An
>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>   Freesurfer mailing list
>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>
>>>>>>>>>   The information in this e-mail is intended only for the
>>>>>>>>   person to
>>>>>>>>>   whom it is
>>>>>>>>>   addressed. If you believe this e-mail was sent to you in
>>>>>>>>   error and
>>>>>>>>>   the e-mail
>>>>>>>>>   contains patient information, please contact the Partners
>>>>>>>>>   Compliance HelpLine at
>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>>>>>   you in error
>>>>>>>>>   but does not contain patient information, please contact the
>>>>>>>>>   sender and properly
>>>>>>>>>   dispose of the e-mail.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>   _______________________________________________
>>>>>>>>   Freesurfer mailing list
>>>>>>>>   Freesurfer@nmr.mgh.harvard.edu <mailto:
>>>>>>> Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> -------------- next part --------------
>>>>>> An HTML attachment was scrubbed...
>>>>>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191118/e0d70211/attachment-0001.html
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 17
>>>>>> Date: Mon, 18 Nov 2019 16:07:40 -0500
>>>>>> From: Vinny K <vinit.k.srivastava@gmail.com>
>>>>>> Subject: Re: [Freesurfer] use of .m3z transform output from
>>>>>>   mri_cvs_register
>>>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <CACUgD2xDPEaoEO6SfJMemQ5On_tTWy=K-r4+_QgXRSQTO7avzA@mail.gmail.com>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>       External Email - Use Caution
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I had mistakenly used the raw moving image in the mri_convert command.  It
>>>>>> should have been the norm.mgz from the moving subject.  The output image
>>>>>> from the mri_convert command now perfectly overlaps with the output from
>>>>>> mri_cvs_register.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Vinny
>>>>>>
>>>>>> On Sat, Nov 16, 2019 at 4:56 PM Vinny K <vinit.k.srivastava@gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I ran the mri_cvs_register between two subjectIDs with very good alignment
>>>>>>> between them.  I had assumed that applying the outputted m3z transform,
>>>>>>> i.e.,final _CVSmorph_toTEMPLATE.m3z, to the moving subjectID (subjb)
>>>>>>> would normalize it to the target subjectID (subja).  That is, the outputted
>>>>>>> image would be the same as the output image from mri_cvs_register
>>>>>>> ,final_CVSmorphed_toTEMPLAT_norm.mgz; however, the resulting image was
>>>>>>> totally out of alignment to the target subjectID.  This is the command I
>>>>>>> had utilized to apply the m3z transform to the moving subjectID:
>>>>>>>
>>>>>>> mri_convert -at
>>>>>>> /home/vinny/Tools/freesurfer/subjects/subjb/cvs/final_CVSmorph_tosubja.m3z
>>>>>>> subjb.nii.gz subjb-to-subja_morph.nii.gz
>>>>>>>
>>>>>>> Thanks for your help,
>>>>>>>
>>>>>>> Vinny
>>>>>>>
>>>>>> -------------- next part --------------
>>>>>> An HTML attachment was scrubbed...
>>>>>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191118/e644a3c7/attachment-0001.html
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 18
>>>>>> Date: Mon, 18 Nov 2019 21:46:26 +0000
>>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID: <cbca25e6-d636-d10c-4224-096f49d5ebaa@mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> why did you call it bert? It just makes things confusing
>>>>>>
>>>>>> On 11/18/19 2:53 PM, An wrote:
>>>>>>> ????????External Email - Use Caution
>>>>>>>
>>>>>>> Here is my recon-all command line:
>>>>>>> recon-all -i ana_Vol.nii -s bert -all
>>>>>>> Many thanks.
>>>>>>>
>>>>>>> Best,
>>>>>>> An
>>>>>>>
>>>>>>>
>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?18??? ??2:33???
>>>>>>>
>>>>>>>   What was your original recon-all command?
>>>>>>>
>>>>>>>   On 11/18/19 1:48 PM, An wrote:
>>>>>>>> ????????External Email - Use Caution
>>>>>>>>
>>>>>>>> I want to map the intensities of the volumes on its corresponding
>>>>>>>> surface in order to get the functional values on each vertex in
>>>>>>>   each
>>>>>>>> frame.?I ran recon-all for the anatomical volume and saved all
>>>>>>>> outputs(mri,labels,surf and etc.) in the bert folder. I use it
>>>>>>>   because
>>>>>>>> I need to specify?the required flag -s in bbregister in order to
>>>>>>>> register the functional volume to its anatomical volume.
>>>>>>>>
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>   ?2019?11?18??? ??1:31???
>>>>>>>> ? ? ?I don't understand what you are trying to do. I'm very
>>>>>>>   confused by
>>>>>>>> ? ? ?your
>>>>>>>> ? ? ?mentioning of bert. What does bert have to do with any of
>>>>>>>   your data?
>>>>>>>> ? ? ?On 11/14/19 10:47 AM, An wrote:
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Oops sorry for the mistakenly?reply. I will pay more attention
>>>>>>>> ? ? ?in the
>>>>>>>> ? ? ?> future.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Bert is the folder with the anatomical data. I tried the
>>>>>>>   following
>>>>>>>> ? ? ?> steps with the 4D volume but failed. Then I checked the
>>>>>>>> ? ? ?registration
>>>>>>>> ? ? ?> result after bbregister and found that the volume was not
>>>>>>>> ? ? ?registered.
>>>>>>>> ? ? ?> After that I tried another 4D volume to do the steps and
>>>>>>>> ? ? ?successfully
>>>>>>>> ? ? ?> got the sampled intensity onto the surface.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> The difference between the new 4D volume I used and the
>>>>>>>   previous
>>>>>>>> ? ? ?one
>>>>>>>> ? ? ?> is that there are two transformation matrices between
>>>>>>>   them. The 4D
>>>>>>>> ? ? ?> dataset that I previously used but failed is the volume
>>>>>>>   already
>>>>>>>> ? ? ?> registered to its anatomical volume(by using others
>>>>>>>   tools). The
>>>>>>>> ? ? ?new 4D
>>>>>>>> ? ? ?> volume that I tried and succeed is the volume not registered.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> I have no idea why the 4D volume after the transformation
>>>>>>>   would
>>>>>>>> ? ? ?cause
>>>>>>>> ? ? ?> a failed result. Could you please let me know that?
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Many thanks.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Best,
>>>>>>>> ? ? ?> An
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>>>>
>>>>>>>> ? ? ??2019?11?13??? ??12:20???
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>? ? ?If you have an anatomical MR that you have run through
>>>>>>>> ? ? ?recon-all,
>>>>>>>> ? ? ?>? ? ?then
>>>>>>>> ? ? ?>? ? ?just use that one instead of bert in your steps below
>>>>>>>> ? ? ?>? ? ?ps. Please remember to post to the FS list and not to us
>>>>>>>> ? ? ?personally
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>? ? ?On 11/12/19 8:41 PM, an wrote:
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Many thanks.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> I got the 4D fMRI dataset from others and it is not raw
>>>>>>>> ? ? ?data. In
>>>>>>>> ? ? ?>? ? ?order
>>>>>>>> ? ? ?>? ? ?> to run mri_vol2surf, I need to calculate the
>>>>>>>   register.dat
>>>>>>>> ? ? ?for the
>>>>>>>> ? ? ?>? ? ?> required flag --srcreg so I tried in this way.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> FYI, the 4D fMRI dataset should have been registered
>>>>>>>   with its
>>>>>>>> ? ? ?>? ? ?> anatomical MR volume by using other tools.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> For now I only ran the recon-all on its anatomical
>>>>>>>   MR volume
>>>>>>>> ? ? ?>? ? ?without
>>>>>>>> ? ? ?>? ? ?> running the functional stream as I don't have the
>>>>>>>   raw data.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Should I also run the raw fMRI data from scratch by
>>>>>>>   using
>>>>>>>> ? ? ?>? ? ?functional
>>>>>>>> ? ? ?>? ? ?> stream? Or if I can run mri_vol2surf independently,
>>>>>>>   which
>>>>>>>> ? ? ?command
>>>>>>>> ? ? ?>? ? ?> should I use to get a register.dat file?
>>>>>>>> ? ? ?>? ? ?> In addition, the intensity of the 4D fMRI dataset I have
>>>>>>>> ? ? ?is between
>>>>>>>> ? ? ?>? ? ?> [-1, 1] and not integers, would this cause any problem?
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Best,
>>>>>>>> ? ? ?>? ? ?> An
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>> ? ? ?>? ? ?>> Don't do the 1st step.
>>>>>>>> ? ? ?>? ? ?>> Why are you registering it to bert? I'm pretty sure
>>>>>>>   bert
>>>>>>>> ? ? ?did not
>>>>>>>> ? ? ?>? ? ?>> participate in your fmri study
>>>>>>>> ? ? ?>? ? ?>> When you run mri_vol2surf, it will probably work
>>>>>>>   better with
>>>>>>>> ? ? ?>? ? ?>> --projfrac 0.5
>>>>>>>> ? ? ?>? ? ?>>
>>>>>>>> ? ? ?>? ? ?>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> Hi Prof. Greve,
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> Thanks for your reply and sorry for the confusion.
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> I have a 4D fMRI dataset with 10 time frames,
>>>>>>>   where the
>>>>>>>> ? ? ?>? ? ?intensity of
>>>>>>>> ? ? ?>? ? ?>>> each voxel is between [-1,1] and not integers. I
>>>>>>>   want to
>>>>>>>> ? ? ?map the
>>>>>>>> ? ? ?>? ? ?>>> intensities of the volumes on its corresponding
>>>>>>>   surface in
>>>>>>>> ? ? ?>? ? ?order to
>>>>>>>> ? ? ?>? ? ?>>> get the functional values on each vertex in each
>>>>>>>   frame.
>>>>>>>> ? ? ?I have
>>>>>>>> ? ? ?>? ? ?>>> already run its corresponding anatomical image in
>>>>>>>> ? ? ?freesurfer.
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> To achieve it, I tried the following steps:
>>>>>>>> ? ? ?>? ? ?>>> 1. conform the fmri series by using mri_convert
>>>>>>>> ? ? ?>? ? ?>>> 2. register the fmri series with the anatomy image
>>>>>>>   by using
>>>>>>>> ? ? ?>? ? ?>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert
>>>>>>>   --reg
>>>>>>>> ? ? ?>? ? ?register.dat
>>>>>>>> ? ? ?>? ? ?>>> 3. assign values from volumes to each vertex by using
>>>>>>>> ? ? ?>? ? ?mri_vol2surf:
>>>>>>>> ? ? ?>? ? ?>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/
>>>>>>>   --srcreg
>>>>>>>> ? ? ?>? ? ?>>> register.dat --hemi lh
>>>>>>>> ? ? ?>? ? ?>>> ? ? I also tried the -regheader in mri_vol2surf:
>>>>>>>> ? ? ?mri_vol2surf
>>>>>>>> ? ? ?>? ? ?--src
>>>>>>>> ? ? ?>? ? ?>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert
>>>>>>>   --hemi lh
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>> ? ? ?>? ? ?freeview. But
>>>>>>>> ? ? ?>? ? ?>>> after step2, the registered volume looks wrong. I am
>>>>>>>> ? ? ?wondering
>>>>>>>> ? ? ?>? ? ?could
>>>>>>>> ? ? ?>? ? ?>>> I use bbregister to register multi-frame fMRI
>>>>>>>   series to
>>>>>>>> ? ? ?a single
>>>>>>>> ? ? ?>? ? ?>>> volume?
>>>>>>>> ? ? ?>? ? ?>>> I also tried to use --regheader to replace the
>>>>>>>   --srcreg
>>>>>>>> ? ? ?file in
>>>>>>>> ? ? ?>? ? ?>>> mri_vol2surf as the output register.dat in step2 is
>>>>>>>> ? ? ?wrong. But
>>>>>>>> ? ? ?>? ? ?the
>>>>>>>> ? ? ?>? ? ?>>> output is still wrong.
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> Many thanks.
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> Best,
>>>>>>>> ? ? ?>? ? ?>>> An
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>>>>> ?2019?11?11???
>>>>>>>> ? ? ???12:16???
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?When you say it is 4D, what do you mean? That
>>>>>>>   each label
>>>>>>>> ? ? ?>? ? ?has its
>>>>>>>> ? ? ?>? ? ?>>>? ? ?own frame?
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> Hi there,
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> I am working with creating a surface
>>>>>>>   parcellation
>>>>>>>> ? ? ?from a
>>>>>>>> ? ? ?>? ? ?>>>? ? ?volumetric
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> parcellation and have some questions as follows:
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> 1. If the volumetric parcellation is a
>>>>>>>   labeled 4D
>>>>>>>> ? ? ?>? ? ?multi-frame
>>>>>>>> ? ? ?>? ? ?>>>? ? ?dataset,
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> could I still use the mris_sample_parc? Or could
>>>>>>>> ? ? ?>? ? ?mri_vol2surf
>>>>>>>> ? ? ?>? ? ?>>>? ? ?get the
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> sampled labels for every vertex?
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> 2. For the 4D multi-frame dataset and
>>>>>>>   mri_vol2surf
>>>>>>>> ? ? ?output
>>>>>>>> ? ? ?>? ? ?>>>? ? ?results,
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> which GUI should I use to visualize it? I tried
>>>>>>>> ? ? ?freeview
>>>>>>>> ? ? ?>? ? ?for 4D
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> multi-frame dataset but it looks weird.
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> 3. Is there any command to separate?multi-frame
>>>>>>>> ? ? ?volume to
>>>>>>>> ? ? ?>? ? ?>>>? ? ?single frame
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> volumes?
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> Many thanks!
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> Best,
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> An
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> _______________________________________________
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>>>? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> ?_______________________________________________
>>>>>>>> ? ? ?>? ? ?>>>? ? ?Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>>>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>>> _______________________________________________
>>>>>>>> ? ? ?>? ? ?>>> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>>>
>>>>>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>>
>>>>>>>> ? ? ?>? ? ?>>
>>>>>>>> ? ? ?>? ? ?>> _______________________________________________
>>>>>>>> ? ? ?>? ? ?>> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>>
>>>>>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>? ? ?The information in this e-mail is intended only for the
>>>>>>>> ? ? ?person to
>>>>>>>> ? ? ?>? ? ?whom it is
>>>>>>>> ? ? ?>? ? ?addressed. If you believe this e-mail was sent to you in
>>>>>>>> ? ? ?error and
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>>>>>>>> ? ? ?>? ? ?contains patient information, please contact the Partners
>>>>>>>> ? ? ?>? ? ?Compliance HelpLine at
>>>>>>>> ? ? ?> http://www.partners.org/complianceline . If the e-mail was
>>>>>>>   sent to
>>>>>>>> ? ? ?>? ? ?you in error
>>>>>>>> ? ? ?>? ? ?but does not contain patient information, please
>>>>>>>   contact the
>>>>>>>> ? ? ?>? ? ?sender and properly
>>>>>>>> ? ? ?>? ? ?dispose of the e-mail.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> _______________________________________________
>>>>>>>> ? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> ? ? ?_______________________________________________
>>>>>>>> ? ? ?Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
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>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>>>>>>>   Freesurfer mailing list
>>>>>>>   Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>>
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>>>>>>> Freesurfer mailing list
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>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 19
>>>>>> Date: Mon, 18 Nov 2019 17:04:32 -0500
>>>>>> From: An <annaqu1024@gmail.com>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <CAJVCUNeKHVUw-22tnVxwUDR6pXh=1_qMuqsiL1qONJTZRSP1kQ@mail.gmail.com>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>       External Email - Use Caution
>>>>>>
>>>>>> Sorry for the confusion, I don't know it has a delicated meaning. I just
>>>>>> followed the steps on the freesurfer download and install webpage to
>>>>>> install the software and then ran the recon-all command.  I will try to
>>>>>> avoid this kind of issues in the future.
>>>>>>
>>>>>> Many thanks.
>>>>>>
>>>>>> Best,
>>>>>> An
>>>>>>
>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> ?2019?11?18??? ??4:47???
>>>>>>
>>>>>>> why did you call it bert? It just makes things confusing
>>>>>>>
>>>>>>> On 11/18/19 2:53 PM, An wrote:
>>>>>>>>       External Email - Use Caution
>>>>>>>>
>>>>>>>> Here is my recon-all command line:
>>>>>>>> recon-all -i ana_Vol.nii -s bert -all
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>>
>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?18??? ??2:33???
>>>>>>>>
>>>>>>>>   What was your original recon-all command?
>>>>>>>>
>>>>>>>>   On 11/18/19 1:48 PM, An wrote:
>>>>>>>>>       External Email - Use Caution
>>>>>>>>>
>>>>>>>>> I want to map the intensities of the volumes on its corresponding
>>>>>>>>> surface in order to get the functional values on each vertex in
>>>>>>>>   each
>>>>>>>>> frame. I ran recon-all for the anatomical volume and saved all
>>>>>>>>> outputs(mri,labels,surf and etc.) in the bert folder. I use it
>>>>>>>>   because
>>>>>>>>> I need to specify the required flag -s in bbregister in order to
>>>>>>>>> register the functional volume to its anatomical volume.
>>>>>>>>>
>>>>>>>>> Many thanks.
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> An
>>>>>>>>>
>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>>   ?2019?11?18??? ??1:31???
>>>>>>>>>   I don't understand what you are trying to do. I'm very
>>>>>>>>   confused by
>>>>>>>>>   your
>>>>>>>>>   mentioning of bert. What does bert have to do with any of
>>>>>>>>   your data?
>>>>>>>>>   On 11/14/19 10:47 AM, An wrote:
>>>>>>>>>>       External Email - Use Caution
>>>>>>>>>>
>>>>>>>>>> Oops sorry for the mistakenly reply. I will pay more
>>>>>>> attention
>>>>>>>>>   in the
>>>>>>>>>> future.
>>>>>>>>>>
>>>>>>>>>> Bert is the folder with the anatomical data. I tried the
>>>>>>>>   following
>>>>>>>>>> steps with the 4D volume but failed. Then I checked the
>>>>>>>>>   registration
>>>>>>>>>> result after bbregister and found that the volume was not
>>>>>>>>>   registered.
>>>>>>>>>> After that I tried another 4D volume to do the steps and
>>>>>>>>>   successfully
>>>>>>>>>> got the sampled intensity onto the surface.
>>>>>>>>>>
>>>>>>>>>> The difference between the new 4D volume I used and the
>>>>>>>>   previous
>>>>>>>>>   one
>>>>>>>>>> is that there are two transformation matrices between
>>>>>>>>   them. The 4D
>>>>>>>>>> dataset that I previously used but failed is the volume
>>>>>>>>   already
>>>>>>>>>> registered to its anatomical volume(by using others
>>>>>>>>   tools). The
>>>>>>>>>   new 4D
>>>>>>>>>> volume that I tried and succeed is the volume not registered.
>>>>>>>>>>
>>>>>>>>>> I have no idea why the 4D volume after the transformation
>>>>>>>>   would
>>>>>>>>>   cause
>>>>>>>>>> a failed result. Could you please let me know that?
>>>>>>>>>>
>>>>>>>>>> Many thanks.
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>> An
>>>>>>>>>>
>>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>>
>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>>>>
>>>>>>>>>   ?2019?11?13??? ??12:20???
>>>>>>>>>>   If you have an anatomical MR that you have run through
>>>>>>>>>   recon-all,
>>>>>>>>>>   then
>>>>>>>>>>   just use that one instead of bert in your steps below
>>>>>>>>>>   ps. Please remember to post to the FS list and not to us
>>>>>>>>>   personally
>>>>>>>>>>   On 11/12/19 8:41 PM, an wrote:
>>>>>>>>>>>       External Email - Use Caution
>>>>>>>>>>>
>>>>>>>>>>> Many thanks.
>>>>>>>>>>>
>>>>>>>>>>> I got the 4D fMRI dataset from others and it is not raw
>>>>>>>>>   data. In
>>>>>>>>>>   order
>>>>>>>>>>> to run mri_vol2surf, I need to calculate the
>>>>>>>>   register.dat
>>>>>>>>>   for the
>>>>>>>>>>> required flag --srcreg so I tried in this way.
>>>>>>>>>>>
>>>>>>>>>>> FYI, the 4D fMRI dataset should have been registered
>>>>>>>>   with its
>>>>>>>>>>> anatomical MR volume by using other tools.
>>>>>>>>>>>
>>>>>>>>>>> For now I only ran the recon-all on its anatomical
>>>>>>>>   MR volume
>>>>>>>>>>   without
>>>>>>>>>>> running the functional stream as I don't have the
>>>>>>>>   raw data.
>>>>>>>>>>> Should I also run the raw fMRI data from scratch by
>>>>>>>>   using
>>>>>>>>>>   functional
>>>>>>>>>>> stream? Or if I can run mri_vol2surf independently,
>>>>>>>>   which
>>>>>>>>>   command
>>>>>>>>>>> should I use to get a register.dat file?
>>>>>>>>>>> In addition, the intensity of the 4D fMRI dataset I
>>>>>>> have
>>>>>>>>>   is between
>>>>>>>>>>> [-1, 1] and not integers, would this cause any problem?
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>> An
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>>>>>> Don't do the 1st step.
>>>>>>>>>>>> Why are you registering it to bert? I'm pretty sure
>>>>>>>>   bert
>>>>>>>>>   did not
>>>>>>>>>>>> participate in your fmri study
>>>>>>>>>>>> When you run mri_vol2surf, it will probably work
>>>>>>>>   better with
>>>>>>>>>>>> --projfrac 0.5
>>>>>>>>>>>>
>>>>>>>>>>>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>>>>>>>       External Email - Use Caution
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Prof. Greve,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks for your reply and sorry for the confusion.
>>>>>>>>>>>>>
>>>>>>>>>>>>> I have a 4D fMRI dataset with 10 time frames,
>>>>>>>>   where the
>>>>>>>>>>   intensity of
>>>>>>>>>>>>> each voxel is between [-1,1] and not integers. I
>>>>>>>>   want to
>>>>>>>>>   map the
>>>>>>>>>>>>> intensities of the volumes on its corresponding
>>>>>>>>   surface in
>>>>>>>>>>   order to
>>>>>>>>>>>>> get the functional values on each vertex in each
>>>>>>>>   frame.
>>>>>>>>>   I have
>>>>>>>>>>>>> already run its corresponding anatomical image in
>>>>>>>>>   freesurfer.
>>>>>>>>>>>>> To achieve it, I tried the following steps:
>>>>>>>>>>>>> 1. conform the fmri series by using mri_convert
>>>>>>>>>>>>> 2. register the fmri series with the anatomy image
>>>>>>>>   by using
>>>>>>>>>>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert
>>>>>>>>   --reg
>>>>>>>>>>   register.dat
>>>>>>>>>>>>> 3. assign values from volumes to each vertex by using
>>>>>>>>>>   mri_vol2surf:
>>>>>>>>>>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/
>>>>>>>>   --srcreg
>>>>>>>>>>>>> register.dat --hemi lh
>>>>>>>>>>>>>   I also tried the -regheader in mri_vol2surf:
>>>>>>>>>   mri_vol2surf
>>>>>>>>>>   --src
>>>>>>>>>>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert
>>>>>>>>   --hemi lh
>>>>>>>>>>>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>>>>   freeview. But
>>>>>>>>>>>>> after step2, the registered volume looks wrong. I am
>>>>>>>>>   wondering
>>>>>>>>>>   could
>>>>>>>>>>>>> I use bbregister to register multi-frame fMRI
>>>>>>>>   series to
>>>>>>>>>   a single
>>>>>>>>>>>>> volume?
>>>>>>>>>>>>> I also tried to use --regheader to replace the
>>>>>>>>   --srcreg
>>>>>>>>>   file in
>>>>>>>>>>>>> mri_vol2surf as the output register.dat in step2 is
>>>>>>>>>   wrong. But
>>>>>>>>>>   the
>>>>>>>>>>>>> output is still wrong.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Many thanks.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Best,
>>>>>>>>>>>>> An
>>>>>>>>>>>>>
>>>>>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>>
>>>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>>
>>>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>
>>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu
>>>>>>>>   <mailto:DGREVE@mgh.harvard.edu>>>>> ?2019?11?11???
>>>>>>>>>   ??12:16???
>>>>>>>>>>>>>   When you say it is 4D, what do you mean? That
>>>>>>>>   each label
>>>>>>>>>>   has its
>>>>>>>>>>>>>   own frame?
>>>>>>>>>>>>>
>>>>>>>>>>>>>   On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>>>>>>>>       External Email - Use Caution
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi there,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I am working with creating a surface
>>>>>>>>   parcellation
>>>>>>>>>   from a
>>>>>>>>>>>>>   volumetric
>>>>>>>>>>>>>> parcellation and have some questions as
>>>>>>> follows:
>>>>>>>>>>>>>> 1. If the volumetric parcellation is a
>>>>>>>>   labeled 4D
>>>>>>>>>>   multi-frame
>>>>>>>>>>>>>   dataset,
>>>>>>>>>>>>>> could I still use the mris_sample_parc? Or
>>>>>>> could
>>>>>>>>>>   mri_vol2surf
>>>>>>>>>>>>>   get the
>>>>>>>>>>>>>> sampled labels for every vertex?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 2. For the 4D multi-frame dataset and
>>>>>>>>   mri_vol2surf
>>>>>>>>>   output
>>>>>>>>>>>>>   results,
>>>>>>>>>>>>>> which GUI should I use to visualize it? I tried
>>>>>>>>>   freeview
>>>>>>>>>>   for 4D
>>>>>>>>>>>>>> multi-frame dataset but it looks weird.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 3. Is there any command to separate multi-frame
>>>>>>>>>   volume to
>>>>>>>>>>>>>   single frame
>>>>>>>>>>>>>> volumes?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Many thanks!
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>> An
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>   Freesurfer mailing list
>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>>>>>>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>
>>>>>>>>>>   The information in this e-mail is intended only for the
>>>>>>>>>   person to
>>>>>>>>>>   whom it is
>>>>>>>>>>   addressed. If you believe this e-mail was sent to you in
>>>>>>>>>   error and
>>>>>>>>>>   the e-mail
>>>>>>>>>>   contains patient information, please contact the Partners
>>>>>>>>>>   Compliance HelpLine at
>>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was
>>>>>>>>   sent to
>>>>>>>>>>   you in error
>>>>>>>>>>   but does not contain patient information, please
>>>>>>>>   contact the
>>>>>>>>>>   sender and properly
>>>>>>>>>>   dispose of the e-mail.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>   _______________________________________________
>>>>>>>>>   Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>   <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>   _______________________________________________
>>>>>>>>   Freesurfer mailing list
>>>>>>>>   Freesurfer@nmr.mgh.harvard.edu <mailto:
>>>>>>> Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> -------------- next part --------------
>>>>>> An HTML attachment was scrubbed...
>>>>>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191118/d835731d/attachment-0001.html
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 20
>>>>>> Date: Mon, 18 Nov 2019 17:14:27 -0500 (EST)
>>>>>> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
>>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation
>>>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <alpine.LRH.2.20.1911181714130.28427@gate.nmr.mgh.harvard.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>> it's not delicate - it's just confusing for us when you use it as it
>>>>>> refers to a specific dataset
>>>>>>
>>>>>> cheers
>>>>>> Bruce
>>>>>> On Mon, 18 Nov 2019, An wrote:
>>>>>>
>>>>>>> ????????External Email - Use Caution????????
>>>>>>>
>>>>>>> Sorry for the confusion, I don't know it has a delicated meaning. I just followed the steps on the
>>>>>>> freesurfer download and install webpage to install the software and then ran the recon-all command.?
>>>>>>> I will try to avoid this kind of issues in the future.
>>>>>>> Many thanks.
>>>>>>>
>>>>>>> Best,
>>>>>>> An
>>>>>>>
>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> ?2019?11?18??? ??4:47???
>>>>>>>     why did you call it bert? It just makes things confusing
>>>>>>>
>>>>>>>     On 11/18/19 2:53 PM, An wrote:
>>>>>>>> ????????External Email - Use Caution
>>>>>>>>
>>>>>>>> Here is my recon-all command line:
>>>>>>>> recon-all -i ana_Vol.nii -s bert -all
>>>>>>>> Many thanks.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> An
>>>>>>>>
>>>>>>>>
>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?18??? ??2:33???
>>>>>>>>
>>>>>>>> ? ? ?What was your original recon-all command?
>>>>>>>>
>>>>>>>> ? ? ?On 11/18/19 1:48 PM, An wrote:
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> I want to map the intensities of the volumes on its corresponding
>>>>>>>> ? ? ?> surface in order to get the functional values on each vertex in
>>>>>>>> ? ? ?each
>>>>>>>> ? ? ?> frame.?I ran recon-all for the anatomical volume and saved all
>>>>>>>> ? ? ?> outputs(mri,labels,surf and etc.) in the bert folder. I use it
>>>>>>>> ? ? ?because
>>>>>>>> ? ? ?> I need to specify?the required flag -s in bbregister in order to
>>>>>>>> ? ? ?> register the functional volume to its anatomical volume.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Many thanks.
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Best,
>>>>>>>> ? ? ?> An
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>> ? ? ??2019?11?18??? ??1:31???
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>? ? ?I don't understand what you are trying to do. I'm very
>>>>>>>> ? ? ?confused by
>>>>>>>> ? ? ?>? ? ?your
>>>>>>>> ? ? ?>? ? ?mentioning of bert. What does bert have to do with any of
>>>>>>>> ? ? ?your data?
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>? ? ?On 11/14/19 10:47 AM, An wrote:
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Oops sorry for the mistakenly?reply. I will pay more attention
>>>>>>>> ? ? ?>? ? ?in the
>>>>>>>> ? ? ?>? ? ?> future.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Bert is the folder with the anatomical data. I tried the
>>>>>>>> ? ? ?following
>>>>>>>> ? ? ?>? ? ?> steps with the 4D volume but failed. Then I checked the
>>>>>>>> ? ? ?>? ? ?registration
>>>>>>>> ? ? ?>? ? ?> result after bbregister and found that the volume was not
>>>>>>>> ? ? ?>? ? ?registered.
>>>>>>>> ? ? ?>? ? ?> After that I tried another 4D volume to do the steps and
>>>>>>>> ? ? ?>? ? ?successfully
>>>>>>>> ? ? ?>? ? ?> got the sampled intensity onto the surface.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> The difference between the new 4D volume I used and the
>>>>>>>> ? ? ?previous
>>>>>>>> ? ? ?>? ? ?one
>>>>>>>> ? ? ?>? ? ?> is that there are two transformation matrices between
>>>>>>>> ? ? ?them. The 4D
>>>>>>>> ? ? ?>? ? ?> dataset that I previously used but failed is the volume
>>>>>>>> ? ? ?already
>>>>>>>> ? ? ?>? ? ?> registered to its anatomical volume(by using others
>>>>>>>> ? ? ?tools). The
>>>>>>>> ? ? ?>? ? ?new 4D
>>>>>>>> ? ? ?>? ? ?> volume that I tried and succeed is the volume not registered.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> I have no idea why the 4D volume after the transformation
>>>>>>>> ? ? ?would
>>>>>>>> ? ? ?>? ? ?cause
>>>>>>>> ? ? ?>? ? ?> a failed result. Could you please let me know that?
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Many thanks.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Best,
>>>>>>>> ? ? ?>? ? ?> An
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>>>>
>>>>>>>> ? ? ?>? ? ??2019?11?13??? ??12:20???
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?If you have an anatomical MR that you have run through
>>>>>>>> ? ? ?>? ? ?recon-all,
>>>>>>>> ? ? ?>? ? ?>? ? ?then
>>>>>>>> ? ? ?>? ? ?>? ? ?just use that one instead of bert in your steps below
>>>>>>>> ? ? ?>? ? ?>? ? ?ps. Please remember to post to the FS list and not to us
>>>>>>>> ? ? ?>? ? ?personally
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?On 11/12/19 8:41 PM, an wrote:
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> Many thanks.
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> I got the 4D fMRI dataset from others and it is not raw
>>>>>>>> ? ? ?>? ? ?data. In
>>>>>>>> ? ? ?>? ? ?>? ? ?order
>>>>>>>> ? ? ?>? ? ?>? ? ?> to run mri_vol2surf, I need to calculate the
>>>>>>>> ? ? ?register.dat
>>>>>>>> ? ? ?>? ? ?for the
>>>>>>>> ? ? ?>? ? ?>? ? ?> required flag --srcreg so I tried in this way.
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> FYI, the 4D fMRI dataset should have been registered
>>>>>>>> ? ? ?with its
>>>>>>>> ? ? ?>? ? ?>? ? ?> anatomical MR volume by using other tools.
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> For now I only ran the recon-all on its anatomical
>>>>>>>> ? ? ?MR volume
>>>>>>>> ? ? ?>? ? ?>? ? ?without
>>>>>>>> ? ? ?>? ? ?>? ? ?> running the functional stream as I don't have the
>>>>>>>> ? ? ?raw data.
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> Should I also run the raw fMRI data from scratch by
>>>>>>>> ? ? ?using
>>>>>>>> ? ? ?>? ? ?>? ? ?functional
>>>>>>>> ? ? ?>? ? ?>? ? ?> stream? Or if I can run mri_vol2surf independently,
>>>>>>>> ? ? ?which
>>>>>>>> ? ? ?>? ? ?command
>>>>>>>> ? ? ?>? ? ?>? ? ?> should I use to get a register.dat file?
>>>>>>>> ? ? ?>? ? ?>? ? ?> In addition, the intensity of the 4D fMRI dataset I have
>>>>>>>> ? ? ?>? ? ?is between
>>>>>>>> ? ? ?>? ? ?>? ? ?> [-1, 1] and not integers, would this cause any problem?
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> Best,
>>>>>>>> ? ? ?>? ? ?>? ? ?> An
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
>>>>>>>> ? ? ?>? ? ?>? ? ?>> Don't do the 1st step.
>>>>>>>> ? ? ?>? ? ?>? ? ?>> Why are you registering it to bert? I'm pretty sure
>>>>>>>> ? ? ?bert
>>>>>>>> ? ? ?>? ? ?did not
>>>>>>>> ? ? ?>? ? ?>? ? ?>> participate in your fmri study
>>>>>>>> ? ? ?>? ? ?>? ? ?>> When you run mri_vol2surf, it will probably work
>>>>>>>> ? ? ?better with
>>>>>>>> ? ? ?>? ? ?>? ? ?>> --projfrac 0.5
>>>>>>>> ? ? ?>? ? ?>? ? ?>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>> On 11/11/2019 1:32 PM, An wrote:
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Hi Prof. Greve,
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Thanks for your reply and sorry for the confusion.
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> I have a 4D fMRI dataset with 10 time frames,
>>>>>>>> ? ? ?where the
>>>>>>>> ? ? ?>? ? ?>? ? ?intensity of
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> each voxel is between [-1,1] and not integers. I
>>>>>>>> ? ? ?want to
>>>>>>>> ? ? ?>? ? ?map the
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> intensities of the volumes on its corresponding
>>>>>>>> ? ? ?surface in
>>>>>>>> ? ? ?>? ? ?>? ? ?order to
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> get the functional values on each vertex in each
>>>>>>>> ? ? ?frame.
>>>>>>>> ? ? ?>? ? ?I have
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> already run its corresponding anatomical image in
>>>>>>>> ? ? ?>? ? ?freesurfer.
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> To achieve it, I tried the following steps:
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> 1. conform the fmri series by using mri_convert
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> 2. register the fmri series with the anatomy image
>>>>>>>> ? ? ?by using
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert
>>>>>>>> ? ? ?--reg
>>>>>>>> ? ? ?>? ? ?>? ? ?register.dat
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> 3. assign values from volumes to each vertex by using
>>>>>>>> ? ? ?>? ? ?>? ? ?mri_vol2surf:
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/
>>>>>>>> ? ? ?--srcreg
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> register.dat --hemi lh
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> ? ? I also tried the -regheader in mri_vol2surf:
>>>>>>>> ? ? ?>? ? ?mri_vol2surf
>>>>>>>> ? ? ?>? ? ?>? ? ?--src
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert
>>>>>>>> ? ? ?--hemi lh
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> The /4Dvol.nii /aligns very well with the orig.mgz in
>>>>>>>> ? ? ?>? ? ?>? ? ?freeview. But
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> after step2, the registered volume looks wrong. I am
>>>>>>>> ? ? ?>? ? ?wondering
>>>>>>>> ? ? ?>? ? ?>? ? ?could
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> I use bbregister to register multi-frame fMRI
>>>>>>>> ? ? ?series to
>>>>>>>> ? ? ?>? ? ?a single
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> volume?
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> I also tried to use --regheader to replace the
>>>>>>>> ? ? ?--srcreg
>>>>>>>> ? ? ?>? ? ?file in
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> mri_vol2surf as the output register.dat in step2 is
>>>>>>>> ? ? ?>? ? ?wrong. But
>>>>>>>> ? ? ?>? ? ?>? ? ?the
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> output is still wrong.
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Many thanks.
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Best,
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> An
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> <mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:DGREVE@mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:DGREVE@mgh.harvard.edu>>>>> ?2019?11?11???
>>>>>>>> ? ? ?>? ? ???12:16???
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?When you say it is 4D, what do you mean? That
>>>>>>>> ? ? ?each label
>>>>>>>> ? ? ?>? ? ?>? ? ?has its
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?own frame?
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?On 11/6/19 5:59 PM, ?? wrote:
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> ????????External Email - Use Caution
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> Hi there,
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> I am working with creating a surface
>>>>>>>> ? ? ?parcellation
>>>>>>>> ? ? ?>? ? ?from a
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?volumetric
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> parcellation and have some questions as follows:
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> 1. If the volumetric parcellation is a
>>>>>>>> ? ? ?labeled 4D
>>>>>>>> ? ? ?>? ? ?>? ? ?multi-frame
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?dataset,
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> could I still use the mris_sample_parc? Or could
>>>>>>>> ? ? ?>? ? ?>? ? ?mri_vol2surf
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?get the
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> sampled labels for every vertex?
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> 2. For the 4D multi-frame dataset and
>>>>>>>> ? ? ?mri_vol2surf
>>>>>>>> ? ? ?>? ? ?output
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?results,
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> which GUI should I use to visualize it? I tried
>>>>>>>> ? ? ?>? ? ?freeview
>>>>>>>> ? ? ?>? ? ?>? ? ?for 4D
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> multi-frame dataset but it looks weird.
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> 3. Is there any command to separate?multi-frame
>>>>>>>> ? ? ?>? ? ?volume to
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?single frame
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> volumes?
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> Many thanks!
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> Best,
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> An
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> _______________________________________________
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?>
>>>>>>>> ? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> ?_______________________________________________
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> _______________________________________________
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>? ? ?>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>>
>>>>>>>> ? ? ?https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>? ? ?>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>> _______________________________________________
>>>>>>>> ? ? ?>? ? ?>? ? ?>> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?>? ? ?>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>>>>>>>> ? ? ?>? ? ?>? ? ?>>
>>>>>>>> ? ? ?https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>? ? ?The information in this e-mail is intended only for the
>>>>>>>> ? ? ?>? ? ?person to
>>>>>>>> ? ? ?>? ? ?>? ? ?whom it is
>>>>>>>> ? ? ?>? ? ?>? ? ?addressed. If you believe this e-mail was sent to you in
>>>>>>>> ? ? ?>? ? ?error and
>>>>>>>> ? ? ?>? ? ?>? ? ?the e-mail
>>>>>>>> ? ? ?>? ? ?>? ? ?contains patient information, please contact the Partners
>>>>>>>> ? ? ?>? ? ?>? ? ?Compliance HelpLine at
>>>>>>>> ? ? ?>? ? ?> http://www.partners.org/complianceline . If the e-mail was
>>>>>>>> ? ? ?sent to
>>>>>>>> ? ? ?>? ? ?>? ? ?you in error
>>>>>>>> ? ? ?>? ? ?>? ? ?but does not contain patient information, please
>>>>>>>> ? ? ?contact the
>>>>>>>> ? ? ?>? ? ?>? ? ?sender and properly
>>>>>>>> ? ? ?>? ? ?>? ? ?dispose of the e-mail.
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?>
>>>>>>>> ? ? ?>? ? ?> _______________________________________________
>>>>>>>> ? ? ?>? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?>? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?>? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?>? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>? ? ?_______________________________________________
>>>>>>>> ? ? ?>? ? ?Freesurfer mailing list
>>>>>>>> ? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>>>>>>> ? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?>
>>>>>>>> ? ? ?> _______________________________________________
>>>>>>>> ? ? ?> Freesurfer mailing list
>>>>>>>> ? ? ?> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> ? ? ?<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> ? ? ?_______________________________________________
>>>>>>>> ? ? ?Freesurfer mailing list
>>>>>>>> ? ? ?Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>>> ? ? ?https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>     _______________________________________________
>>>>>>>     Freesurfer mailing list
>>>>>>>     Freesurfer@nmr.mgh.harvard.edu
>>>>>>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 21
>>>>>> Date: Tue, 19 Nov 2019 01:59:48 +0000
>>>>>> From: An Lijun <lijun.an@hotmail.com>
>>>>>> Subject: Re: [Freesurfer] Volume (WM Parcellation) of
>>>>>>   RightCerebralCortex--Freesurfer 6.0
>>>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <CWXP123MB2182C7D7E2C53FD2999CD0149A4C0@CWXP123MB2182.GBRP123.PROD.OUTLOOK.COM>
>>>>>>  
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>       External Email - Use Caution
>>>>>>
>>>>>> Thanks for your reply!
>>>>>> You mean LeftCerebralCortex is actually lhCortex in aseg.stats, right?
>>>>>>
>>>>>> Best Regards,
>>>>>> An Lijun
>>>>>>
>>>>>>
>>>>>> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> ?2019?11?19??? ??2:20???
>>>>>> You can find it in aseg.stats under
>>>>>>
>>>>>> # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter
>>>>>> volume, 272816.537999, mm^3
>>>>>> # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter
>>>>>> volume, 260016.082731, mm^3
>>>>>> # Measure Cortex, CortexVol, Total cortical gray matter volume,
>>>>>> 532832.620730, mm^3
>>>>>>
>>>>>>
>>>>>> On 11/13/19 11:54 PM, An Lijun wrote:
>>>>>>>       External Email - Use Caution
>>>>>>>
>>>>>>> Dear Freesurfer experts,
>>>>>>>
>>>>>>> I am trying to use ADNI MERGE R package to get 'wholebrain' volume.
>>>>>>>
>>>>>>> It requires <Left/Right>CerebralCortex. The information I get from
>>>>>>> ADNI merge is "*Volume (WM Parcellation) of RightCerebralCortex*".
>>>>>>>
>>>>>>> But when I ran Freesurfer reconall 6.0, I could not
>>>>>>> find <Left/Right>CerebralCortex under 'stats' folder, do you know
>>>>>>> where it could be? Thanks so much.
>>>>>>>
>>>>>>> Best Regards,
>>>>>>> An Lijun
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> -------------- next part --------------
>>>>>> An HTML attachment was scrubbed...
>>>>>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191119/eec6e5aa/attachment-0001.html
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 22
>>>>>> Date: Tue, 19 Nov 2019 10:13:03 +0100
>>>>>> From: fsbuild <fsbuild@contbay.com>
>>>>>> Subject: Re: [Freesurfer] Custom location of license file
>>>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>>>> Cc: khs3z@virginia.edu
>>>>>> Message-ID: <1574154783.5dd3b21f76929@trashmail.com>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>       External Email - Use Caution
>>>>>>
>>>>>> Hello Karsten,
>>>>>>
>>>>>>
>>>>>>
>>>>>> Another option would be to try the 6.0.1 freesurfer release,
>>>>>>
>>>>>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz
>>>>>>
>>>>>>
>>>>>>
>>>>>> I've been told that it works in this release to set the FS_LICENSE environment variable to the path of license.txt
>>>>>>
>>>>>>
>>>>>>
>>>>>> - R.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>           fsbuild        November 15, 2019 at 03:25
>>>>>> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello Karsten,
>>>>>> I
>>>>>> think the location for license.txt in the freesurfer 6 release needs to
>>>>>> be under $FREESURFER_HOME, ie., $FREESURFER_HOME/license.txt, and
>>>>>> cannot be relocated from there by an environment variable. &nbsp;But you can
>>>>>> try using a soft link to point to it in another location. &nbsp;
>>>>>> While
>>>>>> it does not work to preserve $HOME/license.txt as a reference in
>>>>>> another environment variable like FREESURFER_HOME or within a soft link,
>>>>>> I believe the shorthand notation ~/license.txt does work in a soft
>>>>>> link. &nbsp; So in your common installation under $FREESURFER_HOME you could
>>>>>> try,
>>>>>> $ cd $FREESURFER_HOME$ ln -s ~/license.txt license.txt
>>>>>> - and see if freesurfer complains if an individual users $HOME/license.txt (or ~/license.txt) is missing.
>>>>>> In
>>>>>> the newer code base on the freesurfer development branch, it should
>>>>>> work to set the FS_LICENSE environment variable to point to the path of
>>>>>> the license.txt file, but I don?t think that works in the 6.0.0 release.
>>>>>> Ideally,
>>>>>> I think the freesurfer group would prefer if each user signed up for
>>>>>> their own license in order to track usage, so maybe try the soft link.
>>>>>>
>>>>>> - R.
>>>>>>
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> -------------- next part --------------
>>>>>> An HTML attachment was scrubbed...
>>>>>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191119/79a6da66/attachment-0001.html
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> Message: 23
>>>>>> Date: Tue, 19 Nov 2019 10:00:10 +0000
>>>>>> From: "Ferraro, Pilar" <FerraroP@pennmedicine.upenn.edu>
>>>>>> Subject: [Freesurfer] Fwd: surface group analysis with qdec
>>>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>>>> Message-ID:
>>>>>>   <EFCBCEB2-43EF-4B98-9D62-E56C3960D041@pennmedicine.upenn.edu>
>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>
>>>>>>       External Email - Use Caution
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I?ve never got a response to my last email (you can find it below).
>>>>>>
>>>>>> Would you be able to let me know so I can proceed with the analyses?
>>>>>>
>>>>>> Many thanks,
>>>>>>
>>>>>> Pilar
>>>>>>
>>>>>> Inizio messaggio inoltrato:
>>>>>>
>>>>>> Da: "Ferraro, Pilar" <FerraroP@pennmedicine.upenn.edu<mailto:FerraroP@pennmedicine.upenn.edu>>
>>>>>> Oggetto: Fw: surface group analysis with qdec
>>>>>> Data: 14 novembre 2019 3:47:42 PM CET
>>>>>> A: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I'm trying to run a surface based group analysis comparing patients and HC, correcting for disease duration.
>>>>>> I enclose here the fsgd file and the design matrix.
>>>>>> I've followed all the steps of the tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0) with no errors.
>>>>>> However, when I try to run the glm analysis with the following command:
>>>>>>
>>>>>> mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.dur.glmdir
>>>>>>
>>>>>> I get the error:
>>>>>>
>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>>>>>> --------------------------------
>>>>>> Possible problem with experimental design:
>>>>>> Check for duplicate entries and/or lack of range of
>>>>>> continuous variables within a class.
>>>>>>
>>>>>> Of course there is no range for the continuous variable (disease duration) in the control group, so I'm wondering how to overcome this limit and proceed correctly with the glm analysis.
>>>>>>
>>>>>> Many thanks in advance for any help you will provide,
>>>>>>
>>>>>> Pilar
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ________________________________
>>>>>> From: Ferraro, Pilar
>>>>>> Sent: Monday, November 11, 2019 7:07 AM
>>>>>> To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>>>> Subject: surface group analysis with qdec
>>>>>>
>>>>>> Hi!
>>>>>>
>>>>>> I've previously run a comparison between patients and HC using qdec, but now I'd like to correct the analysis for disease duration.
>>>>>> I've therefore generated a second qdec.table.dat file inserting the disease duration column with the following structure:
>>>>>> fsid group duration
>>>>>> Input subj1 1 13
>>>>>> Input subj2 0
>>>>>>
>>>>>> (For healthy controls group (group 0) I've tried both options, leaving the duration column blank or inserting 0 as a value).
>>>>>> I've also left the group.level file the same of the previous analysis.
>>>>>> However, when i open the new qdec.table.dat file with qdec I get problems in correctly uploading the data.
>>>>>> In particular, I get the following error:
>>>>>>
>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
>>>>>> Possible problem with experimental design:
>>>>>> Check for duplicate entries and/or lack of range of continuous variables within a class.
>>>>>> If you seek help with this problem, make sure to send:
>>>>>> This is the command line:
>>>>>> mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh --fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods --glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage lh --label /home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat
>>>>>>
>>>>>> Of course there is no range for the continuous variable (disease duration) in the control group, so I'm wondering how to overcome this and generate a correct qdec.table.dat file.
>>>>>>
>>>>>> Thanks in advance for any help!
>>>>>>
>>>>>> Pilar
>>>>>>
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>>>>>> Desc: lh-Avg-thickness-dur-Cor.mtx
>>>>>> Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191119/3167fda9/attachment-0001.obj
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>> End of Freesurfer Digest, Vol 189, Issue 26
>>>>>> *******************************************
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 9
>>>> Date: Wed, 20 Nov 2019 23:02:18 +0000
>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
>>>> Subject: Re: [Freesurfer] Freesurfer analyses in MATLAB
>>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <327663f6-966a-6f5a-71d5-f53adcb3b7a3@mgh.harvard.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> sorry, I don't know what it is you are doing here. what are beta2 and
>>>> X2? what is DV? what are you plotting against what?
>>>>
>>>> On 11/14/19 3:25 PM, cody samth wrote:
>>>>> ????????External Email - Use Caution
>>>>>
>>>>> Hi I'm interested in running some analyses in matlab using freesurfer
>>>>> commands. I'm running an interaction effect, however I'm having issues
>>>>> residualizing the brain values to plot.
>>>>>
>>>>> For running interaction effects I'm running it by inputting:
>>>>>
>>>>> X=load('Xg.dat')
>>>>> Y=load('ROI.dat')
>>>>> C=load('C.dat')
>>>>> [beta rvar]=fast_glmfit(y,x)
>>>>> [F pvalues]=fast_fratio(beta,X.rvar.C)
>>>>>
>>>>> Which works correctly, then to residualize the values to plot against
>>>>> my DV I was inputting:
>>>>>
>>>>> X=load('Xg.dat')
>>>>> Y=load('ROI.dat')
>>>>> beta=inv(X'*X)*(X'*Y)
>>>>> beta2=load('beta.txt) ; nuisance beta coefficients removed
>>>>> X2=load('X2.dat') ; nuisance columns removed
>>>>> yhat=X2*beta2
>>>>>
>>>>> However the issue I'm having is when plotting the yhat against my
>>>>> variable of interest is that yhat is perfectly?predicted by my DV.
>>>>> This is the case for any ROI I test which makes me suspect i have an
>>>>> error in the matrix somewhere. I've attached a graph and can send the
>>>>> .dat files if needed.
>>>>> Screen Shot 2019-11-14 at 3.08.37 PM.png
>>>>>
>>>>> Thanks,
>>>>> Cody
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 10
>>>> Date: Thu, 21 Nov 2019 07:14:01 +0100
>>>> From: fsbuild <fsbuild@contbay.com>
>>>> Subject: Re: [Freesurfer] Freesurfer 4.5 on Ubuntu 18.04 ?
>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>> Cc: paulo_baptista@brown.edu
>>>> Message-ID: <1574316841.5dd62b29c075d@trashmail.com>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>>       External Email - Use Caution
>>>>
>>>> Hello Paulo,
>>>> What is the location of the freesurfer license file (?), i.e., I would make sure the freesurfer license file is under $FREESURFER_HOME and then see if you get different results running the command.
>>>> Even with the license file though, I?m not sure all the Freesurfer 4 binaries will run on Ubuntu 18
>>>> - R.
>>>> On Nov 19, 2019, at 15:26, Baptista, Paulo &lt;paulo_baptista@brown.edu&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello FreeSurfer Developers,I am helping a researcher in my department run FreeSurfer on a new computer.&nbsp; They insist that it should run on FreeSurfer 4.5 because their old system ran that version.&nbsp; Is the following possible?&nbsp; We can run FreeSurfer 6.0 fine, but they say there are differences between the versions. &nbsp;1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0-full
>>>> 2) Platform: Ubuntu 18.04.1 LTS
>>>> 3) uname -a: Linux clps-pb1 4.15.0-64-generic #73-Ubuntu SMP Thu Sep 12 13:16:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>>>> 4) recon-all.log: n/a Segmentation Fault - see below(base) root@clps-pb1:/var/tmp# cd freesurfer4(base) root@clps-pb1:/var/tmp/freesurfer4# lsASegStatsLUT.txt &nbsp;DefectLUT.txt &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; FreeSurferEnv.sh &nbsp;mni &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;Simple_surface_labels2009.txtAUTHORS &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; diffusion &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; fsafd &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; SegmentNoLUT.txt &nbsp; &nbsp; subjectsaverage &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; docs &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;fsfast &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;sessions &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; tkmeditParcColorsCMAbin &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; FreeSurferColorLUT.txt &nbsp;lib &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; SetUpFreeSurfer.cshbuild-stamp.txt &nbsp; FreeSurferEnv.csh &nbsp; &nbsp; &nbsp; matlab &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;SetUpFreeSurfer.sh(base) root@clps-pb1:/var/tmp/freesurfer4# export FREESURFER_HOME=/var/tmp/freesurfer4(base) root@clps-pb1:/var/tmp/freesurfer4# source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME &nbsp; /var/tmp/freesurfer4FSFAST_HOME &nbsp; &nbsp; &nbsp; /var/tmp/freesurfer4/fsfastFSF_OUTPUT_FORMAT niiSUBJECTS_DIR &nbsp; &nbsp; &nbsp;/var/tmp/freesurfer4/subjectsMNI_DIR &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; /var/tmp/freesurfer4/mni(base) root@clps-pb1:/var/tmp/freesurfer4# cd ..(base) root@clps-pb1:/var/tmp# cd f4bash: cd: f4: No such file or directory(base) root@clps-pb1:/var/tmp# mkdir f4(base) root@clps-pb1:/var/tmp# cd f4(base) root@clps-pb1:/var/tmp/f4# ls(base) root@clps-pb1:/var/tmp/f4# &nbsp;export SUBJECTS_DIR=/var/tmp/f4(base) root@clps-pb1:/var/tmp/f4# cp $FREESURFER_HOME/subjects/sample-001.mgz .(base) root@clps-pb1:/var/tmp/f4# ls -lrttotal 6136-rw-r--r-- 1 r!
 oo!
>> t!
>>> r!
>>>> oot 6280
>>>> 209 Nov 19 15:13 sample-001.mgz(base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz sample-001.nii.gzmri_convert sample-001.mgz sample-001.nii.gz$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $reading from sample-001.mgz...Segmentation fault (core dumped)(base) root@clps-pb1:/var/tmp/f4#Thanks,Paulo_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> -------------- next part --------------
>>>> An HTML attachment was scrubbed...
>>>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191121/03f95c6b/attachment-0001.html
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 11
>>>> Date: Thu, 21 Nov 2019 09:34:36 +0000
>>>> From: Aline Delva <aline.delva@uzleuven.be>
>>>> Subject: [Freesurfer] Substantia nigra delineation
>>>> To: "'freesurfer@nmr.mgh.harvard.edu'"
>>>>     <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID: <4152f89856664506bc9122d2dd6684c5@uzleuven.be>
>>>> Content-Type: text/plain; charset="ks_c_5601-1987"
>>>>
>>>>       External Email - Use Caution
>>>>
>>>> Dear,
>>>>
>>>> We would like to delineate the substantia nigra using a 3D Sag BRAVO and a 3D Sag FLAIR in freesurfer.
>>>> What is the optimal method to do this?
>>>> We already performed recon all and unfortunately SN was not segmented.
>>>>
>>>> Yours sincerely,
>>>>
>>>> Delva Aline, MD
>>>>
>>>> Neurology resident
>>>> UZ Leuven, Belgium
>>>> * aline.delva@uzleuven.be<mailto:aline.delva@uzleuven.be>
>>>>
>>>> PhD student Biomedical sciences
>>>> KU Leuven Department of Neurosciences, Research Group Experimental Neurology, Laboratory for Parkinson Research
>>>> KU Leuven Deparement of Imaging and Pathology, Nuclear Medicine and Molecular Imaging
>>>> * aline.delva@kuleuven.be<mailto:aline.delva@kuleuven.be>
>>>> ?   +32 (0) 16 345771
>>>>
>>>> -------------- next part --------------
>>>> An HTML attachment was scrubbed...
>>>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191121/fb271141/attachment-0001.html
>>>>
>>>> ------------------------------
>>>>
>>>> Message: 12
>>>> Date: Thu, 21 Nov 2019 08:49:24 -0500
>>>> From: "Baptista, Paulo" <paulo_baptista@brown.edu>
>>>> Subject: Re: [Freesurfer] Freesurfer 4.5 on Ubuntu 18.04 ?
>>>> To: fsbuild <fsbuild@contbay.com>
>>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>>> Message-ID:
>>>>     <CAMKPAzhYH_WMS3UcXEZ+Q5zS7xsGWUbEr5kKGV_C_gRDQEtAzA@mail.gmail.com>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>>       External Email - Use Caution
>>>>
>>>> Hello--
>>>>
>>>> Good morning.  Thank you very much for your email.
>>>>
>>>> Yes we have the license file.  When we didn't have the license file, we
>>>> would get an error about missing license file.
>>>>
>>>> (base) pbaptist@clps-pb1:/var/tmp/freesurfer4$ ls
>>>> ASegStatsLUT.txt  bin              diffusion
>>>> FreeSurferEnv.csh  fsfast  mni               SetUpFreeSurfer.csh
>>>> subjects
>>>> AUTHORS           build-stamp.txt  docs                    FreeSurferEnv.sh
>>>> lib     SegmentNoLUT.txt  SetUpFreeSurfer.sh
>>>> tkmeditParcColorsCMA
>>>> average           DefectLUT.txt    FreeSurferColorLUT.txt  fsafd
>>>> matlab  sessions          Simple_surface_labels2009.txt
>>>> (base) pbaptist@clps-pb1:/var/tmp/freesurfer4$ ls -la .license
>>>> -rw-r--r-- 1 root root 49 Nov 18 15:10 .license
>>>> (base) pbaptist@clps-pb1:/var/tmp/freesurfer4$ cat .license
>>>> pb@brown.edu
>>>> 41878
>>>> *C8f07l/gczz6
>>>> FSdMgckdPeGoE
>>>> (base) pbaptist@clps-pb1:/var/tmp/freesurfer4$
>>>>
>>>> (base) root@clps-pb1:/var/tmp/freesurfer4# mv .license license
>>>> (base) root@clps-pb1:/var/tmp/freesurfer4# cd bin
>>>> (base) root@clps-pb1:/var/tmp/freesurfer4/bin#  export
>>>> FREESURFER_HOME=/var/tmp/freesurfer4
>>>> (base) root@clps-pb1:/var/tmp/freesurfer4/bin# source
>>>> $FREESURFER_HOME/SetUpFreeSurfer.sh
>>>> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 --------
>>>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>>> FREESURFER_HOME   /var/tmp/freesurfer4
>>>> FSFAST_HOME       /var/tmp/freesurfer4/fsfast
>>>> FSF_OUTPUT_FORMAT nii
>>>> SUBJECTS_DIR      /var/tmp/freesurfer4/subjects
>>>> MNI_DIR           /var/tmp/freesurfer4/mni
>>>> (base) root@clps-pb1:/var/tmp/freesurfer4/bin# export
>>>> SUBJECTS_DIR=/var/tmp/f4
>>>> (base) root@clps-pb1:/var/tmp/freesurfer4/bin# cd  /var/tmp/f4
>>>> (base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz
>>>> sample-001.nii.gz
>>>> mri_convert sample-001.mgz sample-001.nii.gz
>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>> reading from sample-001.mgz...
>>>> --------------------------------------------------------------------------
>>>> *ERROR: FreeSurfer license file /var/tmp/freesurfer4/.license not found.*
>>>> If you are outside the NMR-Martinos Center,
>>>> go to http://surfer.nmr.mgh.harvard.edu to
>>>> get a valid license file (it's free).
>>>> If you are inside the NMR-Martinos Center,
>>>> make sure to source the standard environment.
>>>> --------------------------------------------------------------------------
>>>> (base) root@clps-pb1:/var/tmp/f4#
>>>>
>>>> *(base) root@clps-pb1:/var/tmp/f4# mv /var/tmp/freesurfer4/license
>>>> /var/tmp/freesurfer4/.license*
>>>> (base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz
>>>> sample-001.nii.gz
>>>> mri_convert sample-001.mgz sample-001.nii.gz
>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>> reading from sample-001.mgz...
>>>> *Segmentation fault (core dumped)*
>>>> (base) root@clps-pb1:/var/tmp/f4#
>>>>
>>>>
>>>> Ok, will you confirm Ubuntu 18 can not run Freesurfer 4?
>>>>
>>>> Thanks,
>>>>
>>>> Paulo
>>>>
>>>>
>>>> On Thu, Nov 21, 2019 at 1:14 AM fsbuild <fsbuild@contbay.com> wrote:
>>>>
>>>>> Hello Paulo,
>>>>>
>>>>> What is the location of the freesurfer license file (?), i.e., I would
>>>>> make sure the freesurfer license file is under $FREESURFER_HOME and then
>>>>> see if you get different results running the command.
>>>>>
>>>>> Even with the license file though, I?m not sure all the Freesurfer 4
>>>>> binaries will run on Ubuntu 18
>>>>>
>>>>> - R.
>>>>>
>>>>> On Nov 19, 2019, at 15:26, Baptista, Paulo <paulo_baptista@brown.edu>
>>>>> wrote:
>>>>>
>>>>>       External Email - Use Caution
>>>>>
>>>>> Hello FreeSurfer Developers,
>>>>>> I am helping a researcher in my department run FreeSurfer on a new
>>>>>> computer..  They insist that it should run on FreeSurfer 4.5 because their
>>>>>> old system ran that version.  Is the following possible?  We can run
>>>>>> FreeSurfer 6.0 fine, but they say there are differences between the
>>>>>> versions.
>>>>>>
>>>>>> 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0-full
>>>>>> 2) Platform: Ubuntu 18.04.1 LTS
>>>>>> 3) uname -a: Linux clps-pb1 4..15.0-64-generic #73-Ubuntu SMP Thu Sep 12 13:16:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>>>>>> 4) recon-all.log: n/a Segmentation Fault - see below
>>>>>>
>>>>>> (base) root@clps-pb1:/var/tmp# cd freesurfer4
>>>>>> (base) root@clps-pb1:/var/tmp/freesurfer4# ls
>>>>>> ASegStatsLUT.txt  DefectLUT.txt           FreeSurferEnv.sh  mni
>>>>>>      Simple_surface_labels2009.txt
>>>>>> AUTHORS           diffusion               fsafd
>>>>>> SegmentNoLUT.txt     subjects
>>>>>> average           docs                    fsfast            sessions
>>>>>>       tkmeditParcColorsCMA
>>>>>> bin               FreeSurferColorLUT.txt  lib
>>>>>> SetUpFreeSurfer.csh
>>>>>> build-stamp.txt   FreeSurferEnv.csh       matlab
>>>>>> SetUpFreeSurfer.sh
>>>>>> (base) root@clps-pb1:/var/tmp/freesurfer4# export
>>>>>> FREESURFER_HOME=/var/tmp/freesurfer4
>>>>>> (base) root@clps-pb1:/var/tmp/freesurfer4# source
>>>>>> $FREESURFER_HOME/SetUpFreeSurfer.sh
>>>>>> -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 --------
>>>>>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>>>>> FREESURFER_HOME   /var/tmp/freesurfer4
>>>>>> FSFAST_HOME       /var/tmp/freesurfer4/fsfast
>>>>>> FSF_OUTPUT_FORMAT nii
>>>>>> SUBJECTS_DIR      /var/tmp/freesurfer4/subjects
>>>>>> MNI_DIR           /var/tmp/freesurfer4/mni
>>>>>> (base) root@clps-pb1:/var/tmp/freesurfer4# cd ..
>>>>>> (base) root@clps-pb1:/var/tmp# cd f4
>>>>>> bash: cd: f4: No such file or directory
>>>>>> (base) root@clps-pb1:/var/tmp# mkdir f4
>>>>>> (base) root@clps-pb1:/var/tmp# cd f4
>>>>>> (base) root@clps-pb1:/var/tmp/f4# ls
>>>>>> (base) root@clps-pb1:/var/tmp/f4#  export SUBJECTS_DIR=/var/tmp/f4
>>>>>> (base) root@clps-pb1:/var/tmp/f4# cp
>>>>>> $FREESURFER_HOME/subjects/sample-001.mgz .
>>>>>> (base) root@clps-pb1:/var/tmp/f4# ls -lrt
>>>>>> total 6136
>>>>>> -rw-r--r-- 1 root root 6280209 Nov 19 15:13 sample-001.mgz
>>>>>> (base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz
>>>>>> sample-001.nii.gz
>>>>>> mri_convert sample-001.mgz sample-001.nii.gz
>>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>>>>>> reading from sample-001.mgz...
>>>>>> Segmentation fault (core dumped)
>>>>>> (base) root@clps-pb1:/var/tmp/f4#
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Paulo
>>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>
>>>>>
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>>>>
>>>> ------------------------------
>>>>
>>>> Message: 13
>>>> Date: Thu, 21 Nov 2019 10:03:04 -0500
>>>> From: An <annaqu1024@gmail.com>
>>>> Subject: [Freesurfer] Map fMRI data onto surface
>>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>> Message-ID:
>>>>     <CAJVCUNc8kM2EFuH_csYPTJcNcb1pPVtfa9Dwjq=7HAS4J8qkiA@mail.gmail.com>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>>       External Email - Use Caution
>>>>
>>>> Hi there,
>>>>
>>>> I want to map the intensities of the fMRI 4D volumes onto its surface in
>>>> order to get the functional values on each vertex in each frame.
>>>>
>>>> I have done the following steps for achieving this:
>>>> 1. ran recon-all on its anatomical volume.
>>>> 2. register the fMRI series with the anatomical volume by using bbregister.
>>>> 3. assign values from volumes to each surface vertex through the command
>>>> mri_vol2surf.
>>>>
>>>> I have got a result of mapping the 4D volumes intensities onto its surfaces
>>>> but there are 35.5% vertices assigned 0 value in every time frame.
>>>>
>>>> I am wondering is the ratio reasonable and how could I improve the result?
>>>> I guess resolution would be one of reasons causing the high 0 value ratio,
>>>> my fMRI data is 2mm^3 and anatomical data is 1mm^3.
>>>>
>>>> Many thanks for your help.
>>>>
>>>> Best,
>>>> An
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>>>>
>>>> ------------------------------
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>> End of Freesurfer Digest, Vol 189, Issue 29
>>>> *******************************************
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 4
>>> Date: Mon, 25 Nov 2019 16:30:08 +0000
>>> From: "Billah, Tashrif" <tbillah@bwh.harvard.edu>
>>> Subject: [Freesurfer] Is -skullstrip set by default?
>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID:
>>>      <CY1PR04MB2377EA8E7BA92D5424FF50ADFF4A0@CY1PR04MB2377.namprd04.prod.outlook.com>
>>>     
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>>
>>> With recon-all, is [-skullstrip](https://surfer.nmr.mgh.harvard.edu/fswiki/skullstrip) option set by default?
>>>
>>> I am trying to understand why there is a separate -noskullstrip option.
>>>
>>> Best,
>>> Tashrif
>>>
>>>
>>>
>>> -------------------------------------------------------------
>>>
>>> Tashrif Billah, MS<https://www.linkedin.com/in/tashrif-billah/>
>>>
>>> Research Engineer
>>>
>>> Brigham and Women's Hospital
>>>
>>> Harvard Medical School
>>>
>>> tbillah@bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu>
>>>
>>> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/
>>> -------------- next part --------------
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>>>
>>> ------------------------------
>>>
>>> Message: 5
>>> Date: Mon, 25 Nov 2019 11:45:29 -0500 (EST)
>>> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] Is -skullstrip set by default?
>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>> Message-ID:
>>>      <alpine.LRH.2.20.1911251145080.28427@gate.nmr.mgh.harvard.edu>
>>> Content-Type: text/plain; charset=US-ASCII; format=flowed
>>>
>>> Hi Tashrif
>>>
>>> in case you have data in which the skull has already been stripped. Yes,
>>> it is on by default
>>>
>>> cheers
>>> Bruce
>>> On Mon, 25 Nov 2019, Billah, Tashrif wrote:
>>>
>>>> With recon-all, is [-skullstrip](https://surfer.nmr.mgh.harvard.edu/fswiki/skullstrip) option set by
>>>> default?
>>>>
>>>> I am trying to understand why there is a separate -noskullstrip option.
>>>>
>>>> Best,
>>>> Tashrif
>>>>
>>>>
>>>> -------------------------------------------------------------
>>>>
>>>> Tashrif Billah, MS
>>>>
>>>> Research Engineer
>>>>
>>>> Brigham and Women's Hospital
>>>>
>>>> Harvard Medical School
>>>>
>>>> tbillah@bwh.harvard.edu
>>>>
>>>> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/
>>>>
>>>>
>>>>
>>>
>>> ------------------------------
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> End of Freesurfer Digest, Vol 189, Issue 34
>>> *******************************************
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> End of Freesurfer Digest, Vol 189, Issue 36
>> *******************************************
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer





------------------------------

Message: 3
Date: Wed, 27 Nov 2019 16:58:45 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] Converting labels drew by freeview to volume
        Error: coordinate mismatch
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <f965ab66-5a79-df95-acff-96ed2cb6aace@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

I'm not sure what the problem is. You say that they match when you load the T1 and the sc. If so, what is the problem?

On 11/27/2019 7:57 AM, zorothustra wrote:

        External Email - Use Caution

Hello Freesurfer Developers,

I'm trying to get superior colliculus' ROI mannually by freeview. I load "orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw the ROI and save it as a label file. After that I use "mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii --s SUB --regheader --noedit --reg register.dat", and it worked, but the coordinate mismatch, much different from the SC's position in the T1 space( Load T1.nii as volume and SC.label as ROI in freeview, and they are matched).
Can anyone help me? Thank you!

1)FreeSurfer version: freesurfer-local-build-dev-20191104
2)platform: Ubuntu 18.04







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*******************************************