Freesurfer

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30132 discussions

[recon-all] [use of -T2] Does only -autorecon3 use -T2?
by Billah, Tashrif 26 Nov '19

26 Nov '19

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(a)bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/

2 1

extract lgi
by Lin Yanyan 26 Nov '19

26 Nov '19

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?

3 2

Regression analysis correcting for 1 variable
by Ferraro, Pilar 26 Nov '19

26 Nov '19

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(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Fwd: surface group analysis with qdec > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <70fa9541-d854-4530-9180-d001cf008f04(a)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(a)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(a)nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>" >>> <freesurfer(a)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(a)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(a)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(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Question about the input for longitudinal > processing pipeline > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <8be29ed9-8627-d005-fd9b-ca3ec56f8a5b(a)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(a)mgh.harvard.edu >> <mailto:DGREVE@mgh.harvard.edu>> >> Subject: Re: [Freesurfer] Question about the input for longitudinal >> ? ? ? ? processing pipeline >> To: "freesurfer(a)nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>" >> <freesurfer(a)nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Message-ID: <d5205fe6-329a-f9b4-252a-8f1857aa42e4(a)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(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Local Gyrification Index: freesurfer version > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <2601bc80-e87a-74b3-9227-24ca60dafd97(a)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(a)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(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Recon-all Error > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <13cb3ba0-0342-6f84-2029-2d4ac0eb914e(a)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(a)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(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] mask for cortical thickness > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <f95d9228-9445-09c0-90d9-48f16e5a41f1(a)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.… > > 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(a)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(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue > 26 > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <453c8556-e0de-cf0e-f84b-65c5273e186e(a)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(a)mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Fw: surface group analysis with qdec >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <b967bd8b-5fb9-0c00-7207-3944fad5c09a(a)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(a)nmr.mgh.harvard.edu <freesurfer(a)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(a)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(a)mgh.harvard.edu> >>> Subject: Re: [Freesurfer] 4D multi-frame parcellation >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <ff691f12-1e79-1b2d-463b-3ae47ace83c2(a)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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)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(a)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(a)mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Multiple comparisons >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <745185b7-5ebb-43bf-6d2d-b7328622fe5f(a)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.… >>> >>> 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(a)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(a)mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Questions for PetSurfer >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <f98e29f6-3532-91ed-021f-1e947468f57f(a)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(a)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(a)mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Cortical thickness values on a vertex base >>> level >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <b9a9830f-fe4d-0321-ede7-1e0a3ee82ca0(a)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(a)nmr.mgh.harvard.edu >>>> <freesurfer-bounces(a)nmr.mgh.harvard.edu> namens Greve, Douglas >>>> N.,Ph.D. <DGREVE(a)mgh.harvard.edu> >>>> *Verzonden:* donderdag 31 oktober 2019 19:16 >>>> *Aan:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)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(a)nmr.mgh.harvard.edu >>>>> <freesurfer-bounces(a)nmr.mgh.harvard.edu> namens Greve, Douglas >>>>> N.,Ph.D. <DGREVE(a)mgh.harvard.edu> >>>>> *Verzonden:* donderdag 31 oktober 2019 16:25 >>>>> *Aan:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)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(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)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(a)mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Question about the input for longitudinal >>> processing pipeline >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <d5205fe6-329a-f9b4-252a-8f1857aa42e4(a)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(a)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(a)mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Brain lobules pooling- request >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <a457c4e8-913e-706e-c7ef-8925c7eaad3d(a)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(a)gmail.com <mailto:samson.nivins@gmail.com> >>>> >>>> *//* >>>> >>>> cid:image001.png@01D4C1F6.9273DF90 >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)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(a)gmail.com> >>> Subject: Re: [Freesurfer] 4D multi-frame parcellation >>> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: >>> <CAJVCUNcDB0ggDRvgbBVYBzftLTdQ42jvUhGhO0+UKe+tkniRoA(a)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(a)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(a)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(a)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(a)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(a)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(a)nmr.mgh.harvard.edu >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)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(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>

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Postdoctoral Opportunity at Brigham and Women’s Hospital – Harvard Medical School
by Lois Gomez, Cristina 26 Nov '19

26 Nov '19

Postdoctoral Opportunity at Brigham and Women’s Hospital – Harvard Medical School The Department of Neurology at Brigham and Women’s Hospital (BWH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals at the post-doctoral level to work on NIH-funded research investigating the physiological and pathological underpinnings behind age and disease related cognitive decline using a multimodal neuroimaging approach. One specific research interest is to investigate the neural underpinnings of memory self-awareness and the progressive dysfunction of these systems that underlies the loss of self-awareness (anosognosia) with Alzheimer’s disease progression. Most of the work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging. KEY RESPONSIBILITIES: The Post-Doctoral Fellow’s responsibilities will include, but are not limited to: * Analyze PET data including amyloid and tau. * Analyze MRI data including functional connectivity, diffusion tractography and structural data. * Model complex datasets including imaging, behavioral and clinical data. * Apply and develop MR and PET acquisition methods for longitudinal analyses. * Lead and assist in the writing of academic manuscripts * Lead and assist in dissemination of research findings through presentations at conferences and for patient and public engagement activities. * Initiate and assist grant applications for further career development. * Assist in mentoring of research assistants. QUALIFICATIONS: * Ph.D. (or close to anticipated PhD) in Neuroscience, Psychology, Engineering or a related field. * Prior experience in brain imaging – PET and/or MRI. * Strong proficiency in various neuroimaging analysis platforms (like FreeSurfer, SPM, FSL), multivariate modeling strategies and connectivity toolboxes. * Established quantitative and statistical skills, including considerable experience in programming in Python and/or Matlab and comfort with diverse computing environments. * Prior background in systems/cognitive neuroscience, neuroanatomy and psychological/clinical constructs is advantageous but not necessary. * A demonstrated capacity to drive first author publications. * Excellent organizational, oral, and written communication skills. ADDITIONAL INFORMATION: This is a 2 to 5 year term position with great opportunities for training in human systems neuroscience, translational/clinical applications and diverse integrated imaging and brain mapping methodologies. The successful candidate will have joint appointments at BWH and HMS and will be closely interacting with the Harvard Aging Brain Study team and especially the group of Dr. Jorge Sepulcre. If interested, please send your CV, letter describing interests, background, qualifications and 3 references (including contact details) to Dr. Patrizia Vannini (patrizia(a)bwh.harvard.edu<mailto:patrizia@bwh.harvard.edu>). BWH & HMS are equal-opportunity, affirmative action employers. Women and minority candidates are encouraged to apply.

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Freesurfer dev version: Hyppocampus, amygdala and thalamus segementation
by Steve Petersen 26 Nov '19

26 Nov '19

External Email - Use Caution Dear Freesurfer devs, We are considering segmenting with the Freesurfer 6 dev version the hippocampus, the amygdala and the thalamus of several subjects who have already done the recon-all. Since we have a T1 image and T2 image with smaller voxel size, we have thought about using the *mode B: segmetation with an additional scan* as explained in the freesurfer webpage. In addition to voxel size, both images have slight differences in acquisition parameters. Taking into account this situation we have these questions: - Since there are other slightly different parameters between image T1 and T2 in addition to voxel size (e.g. matrix size), it is correct to use B mode with additional scan or we should use multispectral segmentation? - Is it necessary to make some previous modification on some image before running the script segment_HA.sh (e.g. coregister both images)? - Is there a quality control that you can recommend after segmenting these structures? Thanks for your help! Best regards,

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How do I fix this white matter boundary issue?
by Taylor, Lisa Marie 26 Nov '19

26 Nov '19

External Email - Use Caution Hi there, I am working on a participant that has abnormally large ventricles. This has previously posed an issue with freesurfer by failing with errors but I have been successful this cycle without the job failing. However, after my first round of edits and running recon-all there is a major issue with the WM and Pial boundary area. I am unaware of how to address it. I have attached images to highlight where my concern is. Any insight? Thank you so much! Lisa ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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V1 length
by Melissa Wright 26 Nov '19

26 Nov '19

External Email - Use Caution Hi everyone, I'm currently using mris_divide_parcellation to create segmentations of V1 by dividing along its long axis. However, I would like to extract the length of this long axis (in mm), in order to compare it with CMF. Would anyone know how best to go about this? Sorry if there's an obvious answer! I have tried looking online and at the function scripts, but no luck. Thank you and best wishes, Melissa E Wright Melissa E Wright, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Maindy Road Cardiff CF24 4HQ UK Tel: +44 (0)29 208 20275 Email: WrightME(a)cardiff.ac.uk<mailto:WrightME@cardiff.ac.uk> Web: Cardiff University webpage<http://www.cardiff.ac.uk/people/research-students/view/482937-> Twitter: @MEW_Neuro Melissa E Wright, MSc Myfyrwraig PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU Ffôn: +44 (0)29 208 20275 E-bost: WrightME(a)caerdydd.ac.uk<mailto:RountreeLC@cardiff.ac.uk>

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freeview parallelized binary
by Clark, Dustin Christopher 26 Nov '19

26 Nov '19

External Email - Use Caution Hello, We recently noticed freeview on the MGH cluster was using multiple cores when loading niftis, however, our local installation only uses one core when loading the same nifiti. Is it possible to get access to this freeview binary or the source code to build it for parallelization on our system? Thank you, Dustin Clark

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linyanyan@outlook.com
by Lin Yanyan 25 Nov '19

25 Nov '19

External Email - Use Caution

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Research Scientist / Engineer 3 position at the University of Washington
by Daniel J Peterson 25 Nov '19

25 Nov '19

External Email - Use Caution The University of Washington Department of Radiology currently has an outstanding opportunity for a RESEARCH SCIENTIST ENGINEER 3. The Research Scientist/Engineer 3 contributes to the growth & success of the Department by executing the mission and vision. The Integrated Brain Imaging Center in the UW Department of Radiology is a research resource center for the interdisciplinary triangle of human MRI based imaging, cognitive neuroscience, and medicine. This is a vibrant multidisciplinary unit working on cutting edge multimodal imaging methods, interoperable software tools, and translation of these approaches to clinical populations. Reporting to the Director of the Integrated Brain Imaging Center (IBIC), this position provides specialized science and research consulting support for the IBIC Research Group within the Department of Radiology. The successful candidate will be one who thrives in a multidisciplinary environment; can maintain a cutting edge conceptual understanding of image processing methods, analysis, and interpretation; views operationalizing methods on science as an exercise in problem solving; and enjoys integrating science and methods, operationally and conceptually. The successful candidate will demonstrate a trajectory of increasing responsibility for facilitating projects requiring divergent intellectual disciplines Please see the full posting for more details: https://uwhires.admin.washington.edu/ENG/Candidates/default.cfm?szCategory=…

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