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30134 discussions

Creating overlay files automatically
by Eloy Geenjaar 31 Oct '16

31 Oct '16

Dear Freesurfer Experts, I am a student at the technical university of Delft and currently working on a project to automatically visualize the cortical thickness data of children. To automatically visualize the data I want to use Freeview, to use Freeview as visualization tool I have to write brain specific layout files. To do this automatically I want to know what the layout for the overlay files is, so Freeview can read them automatically. The data for the layout files should be different per brain, I have already acquired the data and I am ready to write it to a layout file, but I can't figure out what the standard way of writing a layout file is, without having to manually do anything. The language in which I want to write the code is Python. Kind regards, Eloy Geenjaar

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values of 0 in the beta.mgh files
by l.c.b.norbom＠psykologi.uio.no 31 Oct '16

31 Oct '16

Hello Freesurfer Developers, I am having an issue with values of 0 in certain areas of the visual cortex in my beta.mgh files. I am looking at the effect of age on grey/white matter signal intensity contrast (grey devided by white times 100) with gender as a regressor. I ran mri_glmfit with the DODS Matrix 0 0 0.5 0.5 CLASS 1 and 2 were males and females respectively and age in months was the variable. When I look at the beta.mgh files in Freeview there are identical parts of surface which contains 0 even tho there are contrast values in those areas in the contrast surface maps. If I understood correctly the 2 first beta files should be the average contrast for males and females at offset? and the 3rd and 4th should be the slope? So at least the first two files should not contain 0 other than in the medial wall. Any idea what I might be doing wrong? Thank you in advance! Cheers, Linn

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Bug Reporting: mris_long_slopes qdec table not found
by Quinn McLellan 31 Oct '16

31 Oct '16

Dear Freesurfer team, I am trying to perform qdec longitudinal analysis. I have ran produced the template and long files, as well as the longitudinal table. I am currently trying to perform the long_mis_slopes command however I keep getting: ERROR: qdec table /qdec/long.qdec.respsex.table.dat not found or empty? I am using Freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 Platform: OS X El Capitan The table does exist, however, I keep getting the same error. The table has the columns that are specified as being necessary (fsid, fsid-base, and an age column - "days" in my case). Currently it also has a response and sex column. I have changed the age column to "years", changed the location in/out of my subjects folder into a 'qdec' folder within /subjects. I removed the fsid column and received an error output of ERROR: qdec table missing correct column headers? Make sure first column is labeled 'fsid' for the time point and second column is 'fsid-base' to specify the subject tempate (base), e.g.: fsid fsid-base age me1 me 22.3 me2 me 23.2 you1 you 21.6 you2 you 22.5 suggesting that it can see the .dat table. Additionally, from the terminal I can open the table in microsoft excel, pico etc. However, it fails when it tries to parse the table. I have attached a log of the varying attempts I have made to use the long_mris_slopes command. I have also attached what is essentially the .dat table I have been trying to use for your viewing as well. I've searched the list and can't seem to find discussion of this error with regards to the long_mis_slopes command. Am I missing something? Does anyone have any thoughts on how to trouble shoot this? Thank you. Quinn

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Amygdala subfields
by sf 31 Oct '16

31 Oct '16

Hi all, is there any possibility to segment amygdala subfields with freesurfer? Similar to the hippocampal subfields segmentation? Cheers - Sascha

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Obtain images extracted from aseg.mgz that have been corrected for partial volume effects
by Andrea Shafer 31 Oct '16

31 Oct '16

Hello FreeSurfer Developers, I'm attempting to create partial volume (pve) corrected images for some of the subcortical segmentations. I have searched the list and found discussions regarding how the volumes for pve corrected data can be obtained by default with the asegstats2table command, or when using the mri_segstats command with the --pv flag. However, I am wondering if it is possible to save the mixed coefficient map of the pve correction process or save a aseg.mgz file that has been pve corrected? Sincerely, Andrea

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Recon-all Exiting without Error
by Natalie Busby 31 Oct '16

31 Oct '16

Hi, I have just started using FreeSurfer and I am trying to do the subcortical segmentation on some Human Connectome Data. In the command line I typed, 'recon-all -i T1w_acpc_dc_restore_1.25.nii -subjid 100307' The following output was produced: WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux /usr/local/freesurfer/subjects/100306 mri_convert /home/fsuser/Documents/SUBJECTS_DIR/100307/fT1w_acpc_dc_restore_1.25.nii /usr/local/freesurfer/subjects/100306/mri/orig/001.mgz mri_convert /home/fsuser/Documents/SUBJECTS_DIR/100307/fT1w_acpc_dc_restore_1.25.nii /usr/local/freesurfer/subjects/100306/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/fsuser/Documents/SUBJECTS_DIR/100307/fT1w_acpc_dc_restore_1.25.nii... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/100306/mri/orig/001.mgz... #------------------------------------------ Started at Mon Oct 31 10:12:26 EDT 2016 Ended at Mon Oct 31 10:12:31 EDT 2016 #@#%# recon-all-run-time-hours 0.001 recon-all -s 100306 finished without error at Mon Oct 31 10:12:31 EDT 2016 done I was wondering if you knew what the problem was? Thank you! Best wishes, Natalie

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Extend pial surface
by Noah Markowitz 31 Oct '16

31 Oct '16

Hi all, I’m trying to extend the pial surface to include missing GM. Part of the problem is that the wm.mgz seems to include the WM, but does not extend the border of the pial surface. I’ve attached links to pictures of the one of the scans. Any help would be greatly appreciated. Noah Without wm.mgz overlay: http://www.mediafire.com/view/9wsenfq2wdrtvcq/no_mwmask.png <http://www.mediafire.com/view/9wsenfq2wdrtvcq/no_mwmask.png> With mg.mgz overlay: http://www.mediafire.com/view/akdtms78iad5usu/with_wmmask.png <http://www.mediafire.com/view/akdtms78iad5usu/with_wmmask.png>

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[Question for recommended MRI protocols]
by 김정식 31 Oct '16

31 Oct '16

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Pial Problem #2
by Noah Markowitz 31 Oct '16

31 Oct '16

Hi, I just sent a question a few minutes ago but forgot to include an important bit in it. Some pial I’m trying to include doesn’t have WM to add that will push the pial surface back. I attached a link to an example. This happens in the parietal lobe, temporal pole, as well as frontal pole. Any suggestions? Noah http://www.mediafire.com/file/it2ukdeg15pphyk/missing_GM2.png <http://www.mediafire.com/file/it2ukdeg15pphyk/missing_GM2.png> http://www.mediafire.com/view/8x3avz4l9lxpoeg/missing_GM1.png

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Error long_mris_slopes
by tom parker 29 Oct '16

29 Oct '16

Dear FreeSurfers, I've been trying to run a longitudinal cortical thickness analysis in FreeSurfer but unfortunately, so far, it has not worked. After preprocessing the data following the instructions from the tutorial, I tried running: *long_mris_slopes --qdec /Volumes/WD/Long/qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Volumes/WD/Long/* And the following error came out: *Parsing the qdec table: /Volumes/WD/Long/qdec/long.qdec.table.datERROR: qdec table /Volumes/WD/Long/qdec/long.qdec.table.dat not found or empty?* The path is correct and there are no empty lines in the file. When I ran: *mris_preproc --debug --qdec-long qdec/long.qdec.table.dat* This comes out: *set echo = 1 ;set debug = 1 ;set debug = 1breakswbreakswendendwhile ( $#argv != 0 )while ( 2 != 0 )set flag = $argv[1] ; shift ;set flag = --qdec-longshiftswitch ( $flag )switch ( --qdec-long )if ( $#argv == 0 ) goto arg1err ;if ( 1 == 0 ) goto arg1errset fsgdf = $argv[1] ; shift ;set fsgdf = qdec/long.qdec.table.datshiftif ( ! -e $fsgdf ) thenif ( ! -e qdec/long.qdec.table.dat ) thenecho "ERROR: cannot find $fsgdf" ;echo ERROR: cannot find qdec/long.qdec.table.datERROR: cannot find qdec/long.qdec.table.datexit 1 ;exit 1* Do you have any idea why this is happening? Thank you so much!

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