Freesurfer October 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
170 discussions

ROI NumVert
by Daya P 04 Nov '16

04 Nov '16

Hi All, My question is about using mri_label2label. When mapping the labels from one subject to another the number of vertices of each ROI is different. Is that something to be expected? How much of a difference does a number of vertices of 50 compare to 40 have on measures like thickness, grey matter and surface area? I would really appreciate some help Thank you, Daiana R. Pur Research Assistant Canadian Surgical Technologies & Advanced Robotics Brain and Mind Institute Western University London, ON, N6A 5B7 Canada

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tkregister2 + mri_vol2vol do not transform
by Chiara Giacosa 01 Nov '16

01 Nov '16

Dear experts, I am new to freesurfer and I am struggling making transformation of images from one subject to another as well as to a template. I have tried different ways, but I always end up with the original image as if the transformation was never applied. I used tkregister2 from command line and mri_vol2vol. I noticed that the transformation matrices are always the identity matrix in the first 3 columns/rows, no matter what transformation I tell the program to do. I don't think that this makes sense so I wonder if I am doing something wrong or if there might be an issue with the version of tkregister I have. My *commands *are: tkregister2 --mov $subj/mri/orig.mgz --targ my_template/mri/orig.mgz --regheader --reg $subj/reg/orig2templ_tkreg.dat --noedit mri_vol2vol --mov $subj/mri/rh.hand_manual.nii.gz --targ my_template/mri/orig.mgz --o $subj/mri/rh.hand_subj_in_mytempl.mgz --reg $subj/reg/orig2templ_tkreg.dat *Output Matrix *$subj/reg/orig2templ_tkreg.da: subject-unknown 1.000000 1.000000 0.150000 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -1.370635986328125e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 -4.750839233398438e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -1.000000000000000e+00 0 0 0 1 round Contents of my $FREESURFER_HOME/build-stamp.txt file: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Any suggestion will be much appreciated! -- Chiara Giacosa Ph.D. candidate Concordia University

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Re: [Freesurfer] Amygdala subfields
by Dorit Kliemann 31 Oct '16

31 Oct '16

Hi Sascha, yes, we have developed an amygdala nuclei atlas similar to the hippocampal subfields . Its currently being tested and to be implemented (hopefully) soon. Stay tuned. Dorit > From: "sf" <fruehholz(a)gmail.com> > Subject: [Freesurfer] Amygdala subfields > Date: 31 October 2016 at 15:13:21 GMT > To: "'Freesurfer support list'" <freesurfer(a)nmr.mgh.harvard.edu> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > > Hi all, is there any possibility to segment amygdala subfields with freesurfer? Similar to the hippocampal subfields segmentation? > Cheers - Sascha > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Re: [Freesurfer] Recon-all Exiting without Error
by Harms, Michael 31 Oct '16

31 Oct '16

Hi, Is this just an exercise to try to duplicate the HCP processing? Because we’ve already run all subjects (with released structural data) through FreeSurfer for users. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Natalie Busby <natalie.busby(a)manchester.ac.uk<mailto:natalie.busby@manchester.ac.uk>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, October 31, 2016 at 9:30 AM 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>> Subject: [Freesurfer] Recon-all Exiting without Error 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 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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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

1 0

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

2 2

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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Freesurfer October 2016