Freesurfer

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30081 discussions

Hippocampal Subfields Segmentation
by Permesh Dhillon 06 Jul '16

06 Jul '16

Hello FreeSurfer Developers, I’m having issues with the hippocampal subfields segmentation using OS X Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611. I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting an error message : Error:CTF file '/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' failed to open for 'Read' access. Error message: 'Open a zip file for read/modify failed.’ The segmented hippocampal files as described on free surfer wiki cannot be found under the subject ‘mri’ folder. I understand other users have complained of a similar issue within the last week. I’d ve grateful if you could assist me with the issue above. Many thanks Permesh This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Any updates on recon-all GPU support?
by Derek Pisner 05 Jul '16

05 Jul '16

Anyone manage to successfully configure recon-all to run with -use-gpu for recent cuda toolkit versions? I realize cuda support has ceased over the past few years for Freesurfer, but have there been any successful builds for CUDA toolkit versions 6 and up? I am currently looking to configure cuda support on a Tesla K80 GPU, which is part of a small beowulf cluster, which is working wonderfully with FSL's cuda support. Many moons ago, when gpu support was working, I found the -use-gpu option with recon-all to be significantly faster and more practical (for the user) than the -openmp option (which even on a 150 core cluster has provided limited speedup during batch runs). Curious to hear what others have been doing. -Derek

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Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)
by Lars M. Rimol 05 Jul '16

05 Jul '16

Hi Anastasia, I have attached the dmri/bvals and dmri/bvec ("bvals"/"bvecs") and the dmri/dwi_orig.mghdti* files. I don't know if it's a problem but the generated bvec file has commas instead of full stop (0,832 instead of 0.832). The input file (attached: "bvec_rows") has full stop. Another thing is that the generated bvals file has an empty space at the end of the row, which is not there in the input file ("bvals_rows"). thank you! LMR Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals and dmri/bvecs files that get generated look fine too? a.y On Sat, 2 Jul 2016, Lars M. Rimol wrote: Hi, Trying to run trac-all -c dmric_file -prep, I get an error message stating that there are different numbers of entries in the bval and bvec files. I don't understand why, since both have the same number of rows (64). OS = Ubuntu 14.04.4 Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated Tracula and FSL (v 5.0.9). Error message: #@# Tensor fit fr. 01. juli 19:20:29 +0200 2016 dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m /media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016 ---------- I also tried flipping the bvec/bval files, but got the same error. I don't know if there's anything wrong with the bval/bvec files, or if this error message is indicative of some other problem. Is the updated Tracula version only compatible with the dev version of FS? I have attached the bval/bvec files and the trac-all.log. ------------------------------------------------------------------- The contents of the dmric file is: setenv SUBJECTS_DIR /media/lmr2/subjects/DTI set dtroot = /media/lmr2/subjects/DTI/tracula_2016_nativerows set subjlist = (4_FS) set dcmroot = /media/lmr2/subjects/DTI set dcmlist = ( 4/5/1.dcm ) set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv Thank you! yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Apply mris_apply_reg for a label
by Alexandre Routier 05 Jul '16

05 Jul '16

Hello everyone, I have a label for the left hemisphere for my subject but I don't understand the syntax to apply mris_apply_reg on this label to obtain the right hemisphere version. mris_left_right_register was performed to get lh.sphere.left_right and lh.sphere.left_right but I don't know how to use this for the mris_apply_reg command. Thanks in advance for your answer. Alexandre

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Registering scans with different voxel sizes/numbers
by zalewk＠u.washington.edu 05 Jul '16

05 Jul '16

Hello Freesurfer team, I have the unfortunate task of performing longitudinal volumetric analysis on subjects collected on three different scanners with different voxel numbers/sizes. I didn't find this out until attempting to run the longitudinal base and receiving this message: WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. By re-registering the original nifti and recreating the norm.mgz/talairach I can correct the geometry, but FSL's Flirt will only work with niftis and not mgz volumes, ergo I can't re-register the manually edited brainmask/wm volumes properly. I was wondering if there were any freesurfer tools I could use to simply re-register the .mgz volumes to the new norm.mgz? If so, how would I go about doing that? Seeing as the brainmask/wm are both registered to 256^3/1mm anyhow, is this something I should even be concerned about? Thanks, KZ

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retinotopic analysis
by Francesca Strappini 05 Jul '16

05 Jul '16

Hello Freesurfers, Where can I find any documentation about how is retinotopic analysis performed in Freesurfer? Thanks. Best -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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Maps/seed on surafce
by Martin Juneja 05 Jul '16

05 Jul '16

Dear FreeSurfer and SPM experts, I am trying to calculate functional connectivity maps using FreeSurfer pipeline: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… . After defining a seed region on raw anatomical image, I co-registered functional data with anatomical data (as reference) and made sure that the seed is at correct place on both anatomical (top left in attached image) and functional (top right) data. Using SPM, I confirmed co-registration was fine. But after running all the steps of FC, looks like the FC maps are not correct: sig.nii.gz at -fthresh 2 3 (shown at bottom left) because I am not getting significant FC at seed location. Here, bottom right shows the seed location on surface after I convert the seed to fsaverage space (for visualization purpose). Any thoughts, ideas or tips on what went wrong here, would be really appreciated. Thanks.

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Hippocampus & Amygdala Volume Accuracy
by Limachia, Gaurang (NIH/NINDS) [F] 05 Jul '16

05 Jul '16

Hello Bruce, I am uploading the data set to filedrop for you to look over. Can you assist us in determining the optimal method for parcellation of the white and gray matter. We are particularly interested in determining the volume of the hippocampus and amygdala. Are there any special parameters we should use for these structures? Therefore, we want to improve the accuracy of the pial and white matter surfaces. I would greatly appreciate your help. Best Regards, Shyam

1 0

retinotopy analysis documentation
by Francesca Strappini 05 Jul '16

05 Jul '16

Hello Freesurfers, I'm re-posting this question. Where can I find any documentation about how is the retinotopic analysis performed in Freesurfer? Thanks. Best -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

1 0

Order of overlays
by Reza Rajimehr 05 Jul '16

05 Jul '16

Hi, In Tksurfer, we want to show functional activity map and borders of aparc on a surface. The borders of aparc are always drawn on top of the activity map, which sometimes hide small activation blobs. Is it possible to draw the activity map on top of the aparc borders? Reza

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