Freesurfer

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30132 discussions

fixing errors with pial boundary
by Morgan Botdorf 18 Apr '19

18 Apr '19

External Email - Use Caution Dear Freesurfer Experts, I asked about this a few months ago, but didn't receive a reply so thought I would ask again! We have come across several subjects where the pial boundary line does not extend far enough outward and misses some gray matter. We know that control points can be used to fix a similar issue with white matter boundaries. Are there any tools that can be used to fix this type of gray matter error? Thank you, Morgan Botdorf -- Morgan Botdorf, M.S. Graduate Student Neurocognitive Development Lab University of Maryland, College Park mbotdorf(a)terpmail.umd.edu Office: 301.405.5922

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convert aseg to functional space
by Sam W. 18 Apr '19

18 Apr '19

External Email - Use Caution Hi, I just finished reconall and now I'd like to convert the aseg.mgz to native functional space. My first thought was to simply convert the aseg.mgz to native functional space with mri_vol2vol: mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz --o aseg-in-rawavg.nii --regheader Is this a valid procedure to convert the aseg to functional space? I think the recommended way is to register the example_func to anatomical first: bbregister --mov example_func.nii.gz --s sub001 --reg reg.dat and then use mri_vol2vol with the --inv flag mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz --o aseg-in-rawavg.nii --regheader --inv But I'm not sure... Could someone confirm which of the above (or maybe none of them) is correct? Best regards, Sam

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mri_glmfit-sim error correcting for MC for LGI analysis
by C.P.E. Rollins 18 Apr '19

18 Apr '19

External Email - Use Caution Dear Freesurfer Developers, I have a 2-part question: 1) I was advised to use permutation to control for multiple comparisons in an LGI analysis, would you mind elaborating how to do this in command line (in terms of command and parameters)? 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error (attached). I was wondering if you might have any advice? The file /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can view it in freeview. Many thanks, Colleen

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Issue with longitudinal surfaces
by maxime GUILLAUME 18 Apr '19

18 Apr '19

External Email - Use Caution Dear freesurfer experts, I re-send this question because i didn't received (or missed) the answer from the first time i sent it. I am performing a longitudinal study (2 time points, 1 year apart) in patients with Multiple Sclerosis using freesurfer 6.0. After following the tutorial for the CROSS, the BASE (where I only performed few manual edits of the surfaces) and the LONG steps, I am facing a problem with the results of the longitudinal pipeline: If I overlay the final surfaces of the different time points (the white and pial surfaces of the LONG step) on the BASE template using the command given in the fs tutorial, there are important differences between the two time points (see figure attached). This happened only on a subset of my subjects. One of our collaborators in this study suggested that this might be because the patient was positioned differently in the two time points, in particular with respect to the z axis (and indeed the major differences between the two surfaces are in the topmost area of the brain). Does anybody have experienced the same problem? And how can I correct for it? Thank you in advance for your help. (*in the captures surfaces of the first visit are in red and blue and in lighter tones for the second visit)

2 1

Thalamic segmentation
by 郑凤莲 18 Apr '19

18 Apr '19

External Email - Use Caution Hi Expert, In the latest version of FS, I have segmented the thalamic successfully. But I can't use Freeview to show the segmentation map. There is an error :"freeview: /usr/lib/libpng15.so.15:version 'PNG15_0' not found (required by /opt/freesurfer/bin/../lib/qt/lib/libQt5Gui.so.5)". May be I didn't install the latest version of Freeview. However, I can't find this version on Freesurferwiki. Could you share me the install steps and the latest version? Thanks very much for your help. Sincerely, Zheng

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same aparc ROI with mri_label2vol?
by Sam W. 17 Apr '19

17 Apr '19

External Email - Use Caution Hi, I created a series of labels with mri_annotation2label (aparc.a2009s labels) and then created a reg file with: tkregister2 --mov mri/rawavg.mgz --noedit --s bert --regheader --reg register.dat and the volume: mri_label2vol --label labels/lh.G_cingul-Post-dorsal.label --temp mri/rawavg.mgz --subject bert --hemi lh --o roi-in-rawavg.nii.gz --proj frac 0 1 .1 --fillthresh .3 --reg register.dat When I load the roi-in-rawavg.nii.gz and the aparc.a2009+aseg.mgz volume in freeview there are parts of the Cingulum in the aparc.a2009+aseg that are not included in the roi-in-rawavg. Probably this is related to the -fillthresh and -proj thresholds. Is there a way to get exactly the same ROI with mri_label2vol as shown in the aparc.a2008+aseg volume? Best regards, Sam

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same output with vol2vol and label2vol
by Sam W. 17 Apr '19

17 Apr '19

External Email - Use Caution Hi, In a Freesurfer help webpage it says that to convert an image (eg brain.mgz) from freesurfer to anatomical native space (eg rawavg.mgz) we should use mri_vol2vol, but for a segmentation (aseg.mgz) we should use mri_label2vol. I converted the aseg.mgz of bert using both vol2vol and label2vol and found no difference - The resulting output images look exactly the same. Is there really an advantage of using label2vol instead of vol2vol? Thanks! Sam

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correlation analysis
by TMS lab 17 Apr '19

17 Apr '19

External Email - Use Caution mri_glmfit --y lh.t1t2ratio_12CMT_fmed_3sm_decurv.fsavg.mgh --fsgd age_dexterity.fsgd --surf fsaverage lh --C contrast.mtx --o lh_NHPT_T1T2_12CMT_allbrain Il giorno gio 11 apr 2019 alle ore 21:58 Greve, Douglas N.,Ph.D. < DGREVE(a)mgh.harvard.edu> ha scritto: > what is your command line? > > On 4/11/19 3:53 PM, TMS lab wrote: > > > > External Email - Use Caution > > > > Unfortunately I get such error message with the matrix 0 0 0 1 > > ERROR: dimension mismatch between X and contrast contrast.mtx X has > > 3 cols, C has 4 cols > > > > Instead if I use 0 0 1, it works > > > > Best, > > RAFAEL > > That should have failed because it only has 3 values (should have 4). I > > think it should be 0 0 0 1 > > > > > > On 4/11/19 3:20 AM, TMS lab wrote: > > > > > > External Email - Use Caution > > > > > > You are right. I want simply to correlate myelin and nhpt regressing > > > out age. > > > I did it with the following matrix: > > > 0 0 1 > > > And it seems to work. Is it ok this matrix? > > > > > > Thanks a lot > > > Rafael > > > > > > Il giorno gio 11 apr 2019 alle 00:22 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>>> ha scritto: > > > > > > That will compute the average of the Age slope and the NHPT slope. > > > Probably not what you want to do > > > > > > On 4/6/19 12:24 PM, TMS lab wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Dear Freesurfer team, > > > > > > > > I'm running a correlation analysis where I'd like to corelate > > > > myelination and a clinical parameter (NHPT) regressing out the > > > effect > > > > of age. > > > > > > > > My contrast.mtx: 0 0 0.5 0.5 > > > > > > > > This is my FSGD FILE: > > > > GroupDescriptorFile 1 > > > > Title Myelin > > > > Class Main > > > > Variables Age NHPT > > > > Inputfs_CGaMain 19 18.2 > > > > ....... > > > > > > > > Is the matrix ok? > > > > > > > > Thanks > > > > Rafael > > > > > > > > _______________________________________________ > > > > 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(a)nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > RispondiRispondi a tuttiInoltra > > > > > > > > > > > > > > Il giorno gio 11 apr 2019 alle ore 09:20 TMS lab <tmslabna(a)gmail.com > > <mailto:tmslabna@gmail.com>> ha scritto: > > > > You are right. I want simply to correlate myelin and nhpt > > regressing out age. > > I did it with the following matrix: > > 0 0 1 > > And it seems to work. Is it ok this matrix? > > > > Thanks a lot > > Rafael > > > > Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. > > <DGREVE(a)mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> ha scritto: > > > > That will compute the average of the Age slope and the NHPT > > slope. > > Probably not what you want to do > > > > On 4/6/19 12:24 PM, TMS lab wrote: > > > > > > External Email - Use Caution > > > > > > Dear Freesurfer team, > > > > > > I'm running a correlation analysis where I'd like to corelate > > > myelination and a clinical parameter (NHPT) regressing out > > the effect > > > of age. > > > > > > My contrast.mtx: 0 0 0.5 0.5 > > > > > > This is my FSGD FILE: > > > GroupDescriptorFile 1 > > > Title Myelin > > > Class Main > > > Variables Age NHPT > > > Inputfs_CGaMain 19 18.2 > > > ....... > > > > > > Is the matrix ok? > > > > > > Thanks > > > Rafael > > > > > > _______________________________________________ > > > 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 > > > > > > _______________________________________________ > > 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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Re: [Freesurfer] Followup on the mystery of the missing mcprextreg file
by Mcnorgan, Christopher 17 Apr '19

17 Apr '19

External Email - Use Caution Hi Doug, After some false starts, I may have uploaded CM_f.nii.gz to the /transfer/incoming folder (my ftp client reports the upload was complete, but the directory listing afterwards shows 0 files). In the event that my ftp client lied to me about the transfer completing successfully, I have also uploaded the file to my google drive where I’ll let it remain for the next few days if you want to get it from there instead: https://drive.google.com/open?id=1urPlFg3NU56RxtZslgLzk-pXef3Csye1 Thanks, Chris From: "Mcnorgan, Christopher" <cpmcnorg(a)buffalo.edu<mailto:cpmcnorg@buffalo.edu>> Subject: [Freesurfer] Followup on the mystery of the missing mcprextreg file Date: April 16, 2019 at 5:55:28 PM EDT To: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> External Email - Use Caution Hi Doug, For some reason I’m having a problem replying to this list with my reply to your reply. To recap: some of my functional runs are missing the mcprextreg file, and so the GLM with the motion correction parameters is failing. You had asked whether a mc-subjectname-bold.log file exists for these data. These log files do exist, and I’ve tried a couple times to send the log files (1MB attachment rejected). I’m including a google drive link to one of the log files in the hopes that your offer still stands to get to the bottom of why these files are reliably not being created for some runs, while created for other runs collected during the same session: https://drive.google.com/open?id=17GLikK1mzY5uL52TyqlGK0Sa5N5Fy1KY We’ve been acutely aware of how many data frames are in each 4D volume because the scanner has been incorrectly writing that all volumes are 256 frames, though our self-paced experiment terminates earlier to that. We accidentally found the fix to be to open up the header using fsledithd, which then zero-pads the missing data frames until we have 256. However this is the case for all runs, so that doesn’t explain why only some runs are failing. Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/ From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> Subject: Re: [Freesurfer] Followup on the mystery of the missing mcprextreg file Date: April 16, 2019 at 6:03:01 PM EDT 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>> Can you upload the functional volume to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is

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Re: [Freesurfer] Help
by Alvarado,Luis R 17 Apr '19

17 Apr '19

External Email - Use Caution Please disregard this last email. I was trying to make adjustments to my mail list settings by following these instructions from the welcome email: You can also make such adjustments via email by sending a message to: Freesurfer-request(a)nmr.mgh.harvard.edu<mailto:Freesurfer-request@nmr.mgh.harvard.edu> with the word `help' in the subject or body (don't include the quotes), and you will get back a message with instructions. Luis R. Alvarado Ph.D. Candidate Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Kentucky Spinal Cord Injury Research Center 220 Abraham Flexner Way, Suite 1500 Louisville, KY 40202

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