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 CautionHi 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
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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 aseries of MRI scans from a single patient. However, after
looking atthe scans, i realized that for most time points, the patient
doesn'thave 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
pipelinein particular on T1 MPRAGE scans that have a contrast agent, or
thatare mp2rage instead of MPRAGE?
Thanks in advance! Best, Darko
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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,
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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
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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/MultipleComparisonsV6.0...
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
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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 CautionThank 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
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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
orderto 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
withoutrunning the functional stream as I don't have the raw data.
Should I also run the raw fMRI data from scratch by using
functionalstream? 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
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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/MultipleComparisonsV6.0...
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.
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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
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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:
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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:
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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
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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:
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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
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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:
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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
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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 CautionI 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 CautionOops 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>
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