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Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue 26
by Ferraro, Pilar 20 Nov '19

20 Nov '19

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 >

2 1

mask for cortical thickness
by Gwang-Won Kim 20 Nov '19

20 Nov '19

2 1

Local Gyrification Index: freesurfer version
by Steve Petersen 20 Nov '19

20 Nov '19

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,

2 1

Re: [Freesurfer] Question about the input for longitudinal processing pipeline
by Darko Komnenić 20 Nov '19

20 Nov '19

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> > 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 > > > > > >

2 1

surface group analysis with qdec
by Ferraro, Pilar 20 Nov '19

20 Nov '19

External Email - Use Caution 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

2 5

Volume (WM Parcellation) of RightCerebralCortex--Freesurfer 6.0
by An Lijun 20 Nov '19

20 Nov '19

External Email - Use Caution Dear Freesurfer experts, I am trying to use ADNI MERGE R package to get 'wholebrain' volume. It requires <Left/Right>CerebralCortex. The information I get from ADNI merge is "Volume (WM Parcellation) of RightCerebralCortex". But when I ran Freesurfer reconall 6.0, I could not find <Left/Right>CerebralCortex under 'stats' folder, do you know where it could be? Thanks so much. Best Regards, An Lijun

2 3

Recon-all error
by Meena M. Makary 19 Nov '19

19 Nov '19

External Email - Use Caution Dear, -- — *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>

1 0

Freesurfer 4.5 on Ubuntu 18.04 ?
by Baptista, Paulo 19 Nov '19

19 Nov '19

External Email - Use Caution > Hello FreeSurfer Developers, > > I am helping a researcher in my department run FreeSurfer on a new > computer. They insist that it should run on FreeSurfer 4.5 because their > old system ran that version. Is the following possible? We can run > FreeSurfer 6.0 fine, but they say there are differences between the > versions. > > 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0-full > 2) Platform: Ubuntu 18.04.1 LTS > 3) uname -a: Linux clps-pb1 4.15.0-64-generic #73-Ubuntu SMP Thu Sep 12 13:16:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux > 4) recon-all.log: n/a Segmentation Fault - see below > > (base) root@clps-pb1:/var/tmp# cd freesurfer4 > (base) root@clps-pb1:/var/tmp/freesurfer4# ls > ASegStatsLUT.txt DefectLUT.txt FreeSurferEnv.sh mni > Simple_surface_labels2009.txt > AUTHORS diffusion fsafd > SegmentNoLUT.txt subjects > average docs fsfast sessions > tkmeditParcColorsCMA > bin FreeSurferColorLUT.txt lib > SetUpFreeSurfer.csh > build-stamp.txt FreeSurferEnv.csh matlab > SetUpFreeSurfer.sh > (base) root@clps-pb1:/var/tmp/freesurfer4# export > FREESURFER_HOME=/var/tmp/freesurfer4 > (base) root@clps-pb1:/var/tmp/freesurfer4# source > $FREESURFER_HOME/SetUpFreeSurfer.sh > -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /var/tmp/freesurfer4 > FSFAST_HOME /var/tmp/freesurfer4/fsfast > FSF_OUTPUT_FORMAT nii > SUBJECTS_DIR /var/tmp/freesurfer4/subjects > MNI_DIR /var/tmp/freesurfer4/mni > (base) root@clps-pb1:/var/tmp/freesurfer4# cd .. > (base) root@clps-pb1:/var/tmp# cd f4 > bash: cd: f4: No such file or directory > (base) root@clps-pb1:/var/tmp# mkdir f4 > (base) root@clps-pb1:/var/tmp# cd f4 > (base) root@clps-pb1:/var/tmp/f4# ls > (base) root@clps-pb1:/var/tmp/f4# export SUBJECTS_DIR=/var/tmp/f4 > (base) root@clps-pb1:/var/tmp/f4# cp > $FREESURFER_HOME/subjects/sample-001.mgz . > (base) root@clps-pb1:/var/tmp/f4# ls -lrt > total 6136 > -rw-r--r-- 1 root root 6280209 Nov 19 15:13 sample-001.mgz > (base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz > sample-001.nii.gz > mri_convert sample-001.mgz sample-001.nii.gz > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from sample-001.mgz... > Segmentation fault (core dumped) > (base) root@clps-pb1:/var/tmp/f4# > > > Thanks, > > Paulo >

1 0

PhD position
by Dídac Vidal 19 Nov '19

19 Nov '19

External Email - Use Caution At the Center for Lifespan Changes in Brain and Cognition, University of Oslo, Norway, we have an available PhD fellowship for a candidate highly interested in (functional) neuroimaging analysis and cognitive neuroscience research. The PhD researcher will focus on investigating the functional mechanisms supporting lifespan changes in cognition. Cognitive functions of interest are episodic memory operations, spatial navigation, and spatial working memory. The Ph.D. fellow will work on large, longitudinal multimodal data, including task fMRI and state-of-the-art sequences. The fellowship is for a period of three or four years. The application deadline is: 10.12.2019 Please see more info here: https://www.jobbnorge.no/en/available-jobs/job/178345/phd-fellowship-in-fun… P.S. Interested candidates are welcome to contact Didac Vidal-Pineiro ( d.v.pineiro(a)psykologi.uio.no) or Anders M Fjell (andersmf(a)psykologi.uio.no) All the best, Dídac -- Dídac Vidal Piñeiro

1 0

Re: [Freesurfer] Custom location of license file
by fsbuild 19 Nov '19

19 Nov '19

External Email - Use Caution Hello Karsten, Another option would be to try the 6.0.1 freesurfer release, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Lin… I've been told that it works in this release to set the FS_LICENSE environment variable to the path of license.txt - R. fsbuild November 15, 2019 at 03:25         External Email - Use Caution        Hello Karsten, I think the location for license.txt in the freesurfer 6 release needs to be under $FREESURFER_HOME, ie., $FREESURFER_HOME/license.txt, and cannot be relocated from there by an environment variable.  But you can try using a soft link to point to it in another location.   While it does not work to preserve $HOME/license.txt as a reference in another environment variable like FREESURFER_HOME or within a soft link, I believe the shorthand notation ~/license.txt does work in a soft link.   So in your common installation under $FREESURFER_HOME you could try, $ cd $FREESURFER_HOME$ ln -s ~/license.txt license.txt - and see if freesurfer complains if an individual users $HOME/license.txt (or ~/license.txt) is missing. In the newer code base on the freesurfer development branch, it should work to set the FS_LICENSE environment variable to point to the path of the license.txt file, but I don’t think that works in the 6.0.0 release. Ideally, I think the freesurfer group would prefer if each user signed up for their own license in order to track usage, so maybe try the soft link. - R. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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