Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30098 discussions

Re: [Freesurfer] [Fsdev] [PATCH] fix ups for DESTDIR
by Z K 23 Feb '16

23 Feb '16

Hello Yaroslav, It the case when "some subdirs makefiles do not care about DESTDIR, which is generally respected by autotools" an autotools version issue? Or related to something else completely? I see that making the change on my end does not produce any ill effects, but I would like to observe the behavior before committing the "fix". -Zeke On 02/22/2016 11:33 PM, Yaroslav Halchenko wrote: > Dear FS Developers, > > Per ZK's blessing I am moving my "whining"... khe khe... dialogue over > to fsdev mailing list. And would like to begin with this patch which > have got buried in the users' mailing list: > > I have got into a problem that currently some subdirs makefiles do not > care about DESTDIR, which is generally respected by autotools... > attached patch should help to make FS 'installable' e.g. via > > make install DESTDIR=$PWD/INSTALL-DIR/ > > NB in the future, it would be a nice "test" to add to .travis.yml > upon successful build, without system wide installation with sudo ;) > > Please review/adopt/accept. > > With best regards, > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > > > _______________________________________________ > Fsdev mailing list > Fsdev(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fsdev >

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FreeSurfer group analysis: mri_glmfit-sim
by Silas 23 Feb '16

23 Feb '16

Dear FS team, I'm currently making a group analysis using the "command-line" group analysis stream in freesurfer. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng [https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> FsTutorial/GroupAnalysisDng - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng> surfer.nmr.mgh.harvard.edu Introduction. This tutorial is designed to introduce you to the "command-line" group analysis stream in FreeSurfer (as opposed to QDEC which is GUI-driven), including ... 1) I would like to do a surface based analysis where i'm only investigating a certain area or label - instead of doing a whole brain analysis. This can be done by introducing --label surface_area_of_interest.label when running mri_glmfit. Would this give me different results from doing a whole brain analysis - or would it just exclude the results from outside the label? And how about after clusterwise correction for multiple comparisons? -> is there a better way to do this than following the command-line group analysis stream in freesurfer? 2) When running mri_glmfit-sim i'm investigating the output ending with -voxel.mgh - how do i interpret the results of this file? When investigating the file in freeview what is the meaning of the units when configuring the overlay? Best, Silas

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Convert spm volume to fresurfer surface
by Daniel Baena Pérez 23 Feb '16

23 Feb '16

Dear Fresurfer users, I would like to analyze group differences in cortical thickness in fresurfer by using as a mask a volumetric SPM activity image. Which command should be used for this purpose? Thanks a lot and best wishes, Sofia

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Still age corrected?
by Daniel Baena Pérez 23 Feb '16

23 Feb '16

Dear Freesurfer user, We have performed group contrasts on cortical thickness correcting by age. Now we want to use the mean cortical thickness of one of the significant clusters as a regressor in other analysis, but we do not know whether the mean cortical thickness value for each subject within this ROI is corrected by age or not. Best regards and thank you

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Regarding: 1.5T images
by Dr Sampada Sinha 23 Feb '16

23 Feb '16

Hello freesurfer experts, I am trying to do T1w analysis using freesurfer. The raw images are in dicom format. However, when I view those raw dicom images, some of the brain areas are missing. I just wanted to ask if there is any tool to reconstruct those missing brain areas in the raw images using freesurfer or I need to discard those participants scan altogether? Also, because the resolution is not good with 1.5T, I have seen that skull stripping is not good with a large chunk of skull tissue coming in the processed images. I tried to adjust the watershed parameters and somehow it worked, but it wasn't satisfactory. I tried to run it through fsl bet and got a good skull strip. However, after running the recon-all followed by auorecon11 no skull strip command the with autorecon2 and autorecon3 I am getting excessive topologic defect. I am attaching the log file with this email for your perusal Will greatly appreciate if I can be helped regarding these two problems I am presently facing with the analysis. Thanks and regards, Sampada Pre-doctoral student India

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control points function
by Kiersten Snyder 23 Feb '16

23 Feb '16

Hello, I am new to using Freesurfer and am currently using it for a biomedical image processing class. I am working on a project and would like to know the image processing technique behind the Control Points function. Is it region growing, or what other process? Thanks for the help! Kiersten

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Ris: eTIV question
by angela.favaro＠unipd.it 23 Feb '16

23 Feb '16

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Read_surf error in reading "lh.seghead" head surface created from "mkheadsurf"
by Maheen Siddiqui 22 Feb '16

22 Feb '16

Dear FreeSurfer users, I have used the "mkheadsurf" function to create "lh.seghead" in the surf folder of my subject. Now I am trying to extract the vertices and faces of "lh.seghead" in the following way: *[vertex_coords, faces] = read_surf('lh.seghead')* but get an error in read_surf which is: *Undefined function or variable "faces".* * Error in read_surf (line 80)* * faces = faces+1;* After a bit of investigation I found that the "magic" number of the file is 16777213 while the triangle magic number is 16777214. Since these are unequal, it doesn't go into the if statement where faces are defined. When I try to changed the magic number manually to be the same as the triangle magic number, I get the following error: *Error using reshape* * To RESHAPE the number of elements must not change.* * Error in read_surf (line 76)* * faces = reshape(faces, 3, fnum)' ;* But I don't think making this change is a good idea as it would affect the surfaces that I try to read that DO have magic number that is actually equal to the triangle magic number. Does anybody know why this might be happening? Any suggestions for me to try? The read_surf works fine when I use it for the pial surface, just not the lh.seghead. I am using FreeSurfer version 5.3.0. I would appreciate any advice! Thanks, Maheen

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Multiple Frames Error
by Marissa Pifer 22 Feb '16

22 Feb '16

Hi freesurfers, I am trying to run the recon-all command on a T1 weighted structural image for one of my subjects and I keep getting this error "Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz has 2 frames Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64 recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 11:13:26 EST 2016" I looked through the mailing list and saw that a few other people have had this problem as well, and I tried some of the solutions that were suggested but still have not been able to get past this. I have run the recon-all command on all of the other subjects in our data set, and none of them have this problem. Not sure what is different about this scan. Anyone run into this problem and were able to fix it? Thanks in advance, Marissa

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Re: [Freesurfer] qdec
by levi solomyak 22 Feb '16

22 Feb '16

Hi Douglas, Sure! Below is the terminal outputs when I try and run the command you suggested on the first five subjects. Any help you could provide would be much appreciated! Best, LS $asegstats2table --common-segs --meas volume --tablefile /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects Parsing the .stats files Traceback (most recent call last): File "/Applications/freesurfer/bin/asegstats2table", line 538, in <module> id_name_map, measurelist = parsed.parse(options.meas) File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse On Fri, Feb 19, 2016 at 2:53 PM, levi solomyak <lsolomyak(a)gmail.com> wrote: > Hi Douglas, > > Sure! Below is the terminal outputs when I try and run the command you > suggested on the first five subjects. Any help you could provide would be > much appreciated! > > Best, > LS > > $asegstats2table --common-segs --meas volume --tablefile > /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat > --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 > SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects > Parsing the .stats files > Traceback (most recent call last): > File "/Applications/freesurfer/bin/asegstats2table", line 538, in > <module> > id_name_map, measurelist = parsed.parse(options.meas) > File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse > > On Fri, Feb 19, 2016 at 2:47 PM, levi solomyak <lsolomyak(a)gmail.com> > wrote: > >> Hi Douglas, >> >> Sure! Below is the terminal outputs when I try and run the command you >> suggested on the first five subjects. Any help you could provide would be >> much appreciated! >> >> Best, >> LS >> >> $asegstats2table --common-segs --meas volume --tablefile >> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat >> --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 >> SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects >> Parsing the .stats files >> Traceback (most recent call last): >> File "/Applications/freesurfer/bin/asegstats2table", line 538, in >> <module> >> id_name_map, measurelist = parsed.parse(options.meas) >> File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse >> self.id_name_map[seg] = strlst[4] # Col 4 is Seg Name >> IndexError: list index out of range >> >> >> >> On Mon, Dec 21, 2015 at 6:13 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu> wrote: >> >>> Can you run the command below outside of qdec and send us the error it >>> prints to the terminal? >>> >>> asegstats2table --common-segs --meas volume --tablefile >>> >>> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat >>> --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 >>> 111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 >>> 117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 >>> 171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 >>> 200109 200614 201111 201414 201818 203418 204016 204521 304020 307127 >>> 308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 >>> 412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 >>> 531536 540436 561242 562446 565452 566454 567052 567961 568963 571548 >>> 580044 580347 581349 583858 586460 594156 598568 599671 >>> >>> >>> >>> On 12/14/2015 02:15 PM, levi solomyak wrote: >>> > Dear experts, >>> > >>> > I've been attempting to generate a stats data table in qdec, but each >>> > time I get a "Index Error: list index is out of range" error. This is >>> > occurring when it is trying to parse the .stats file. >>> > >>> > I've made sure that the files all line up exactly with the qdec table >>> > and that SUBJECTS_DIR is properly sourced so I'm not sure how to fix >>> > this problem. Any help would be greatly appreciated! >>> > >>> > >>> > Here are the details of the errors: >>> > >>> > 1) machine being used: Linux localhost.localdomain >>> > 3.10.0-229.4.2.el7.x86_64 #1 SMP Wed May 13 10:06:09 UTC 2015 x86_64 >>> > x86_64 x86_64 GNU/Linux >>> > 2) Freesurfer version: >>> > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP >>> > 3) Current working directory: >>> /projects/IndivRITL/data/leviDiff/Subjects >>> > 4) which qdec : /usr/local/freesurfer/bin/qdec >>> > 5) After loading the gui, I attempted to generate a qdec stats table. >>> > This is the error that was returned: >>> > >>> > >>> ----------------------------------------------------------------------------------- >>> > asegstats2table --common-segs --meas volume --tablefile >>> > >>> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat >>> > --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 >>> > 111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 >>> > 117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 >>> > 171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 >>> > 200109 200614 201111 201414 201818 203418 204016 204521 304020 307127 >>> > 308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 >>> > 412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 >>> > 531536 540436 561242 562446 565452 566454 567052 567961 568963 571548 >>> > 580044 580347 581349 583858 586460 594156 598568 599671 >>> > SUBJECTS_DIR : /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects >>> > Parsing the .stats files >>> > Traceback (most recent call last): >>> > File "/usr/local/freesurfer/bin/asegstats2table", line 538, in >>> <module> >>> > id_name_map, measurelist = parsed.parse(options.meas) >>> > File "/home/usr/local/freesurfer/bin/fsutils.py", line 115, in parse >>> > self.id_name_map[seg] = strlst[4] # Col 4 is Seg Name >>> > IndexError: list index out of range >>> > ERROR: In >>> > >>> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, >>> > line 230 >>> > vtkKWQdecApp (0x278d8060): >>> > Script: >>> > vtkTemp2 GenerateStatsDataTables >>> > Returned Error on line 1: >>> > Uncaught exception: command failed: asegstats2table --common-segs >>> > --meas volume --tablefile >>> > >>> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat >>> > --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 >>> > 111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 >>> > 117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 >>> > 171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 >>> > 200109 200614 201111 201414 201818 203418 204016 204521 304020 307127 >>> > 308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 >>> > 412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 >>> > 531536 540436 561242 562446 565452 566454 567052 567961 568963 571548 >>> > 580044 580347 581349 583858 586460 594156 598568 599671 >>> > >>> > Stack trace: >>> > Uncaught exception: command failed: asegstats2table --common-segs >>> > --meas volume --tablefile >>> > >>> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat >>> > --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 >>> > 111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 >>> > 117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 >>> > 171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 >>> > 200109 200614 201111 201414 201818 203418 204016 204521 304020 307127 >>> > 308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 >>> > 412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 >>> > 531536 540436 561242 562446 565452 566454 567052 567961 568963 571548 >>> > 580044 580347 581349 583858 586460 594156 598568 599671 >>> > >>> > while executing >>> > "vtkTemp2 GenerateStatsDataTables" >>> > >>> ------------------------------------------------------------------------------------------------------- >>> > >>> > >>> > >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer(a)nmr.mgh.harvard.edu >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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. >>> >>> >> >> >> >> > > > -- > Levi Solomyak > Cole Neuroscience Laboratory (*colelab.org <http://colelab.org/>*) > Center for Molecular and Behavioral Neuroscience (CMBN) > Rutgers-Newark University > -- Levi Solomyak Cole Neuroscience Laboratory (*colelab.org <http://colelab.org/>*) Center for Molecular and Behavioral Neuroscience (CMBN) Rutgers-Newark University

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