Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

Longitudinal MRI but different scanner
by Shane Schofield 22 Dec '17

22 Dec '17

Hi Freesurfer Team, I try to calculate a within-subject decrease in cortical thickness over 2 years, but the MRI scanner was changed during the project. Is it still possible to do that using the longitudinal stream in Freesurfer? Thanks. Best Wishes,Shane

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error in Talairach transformation
by 박경일 21 Dec '17

21 Dec '17

Dear experts, I have some problems in running recon-all. Recon-all process was stopped with this error message ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string." I guess this is because of low resolution or small size of images. Hopefully you can confirm why. Thank you so much for you help in advance. FYI, log file is attached. -- Kyung

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Segmentation fault (core dumped)
by Uquillas, Federico D'Oleire 21 Dec '17

21 Dec '17

Dear FreeSurfer experts, I am unable to run the qcache procedure and was wondering if anybody could help me find what is going on. I've tried running qcache with several versions of the fsaverage (e.g., fsaverage5, fsaverage6, fsaverage), and have also tried running it in a variety of subjects but they all crash. Thank you so much for you help. All the best, Fred

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Contrast to Noise Ratio - mri_glmfit vs. selxavg3-sess
by shahin＠nmr.mgh.harvard.edu 21 Dec '17

21 Dec '17

Hi Surfers, As you know, there are multiple ways to measure contrast to noise ration (CNR). I am trying to understand how is cnr.nii generated as an output from mri_glmfit command. I also noticed that, cnr.nii values are mostly NaN when I have one subject only. I am wondering why it is not the same as cnr.nii generated by selxavg3-sess for the same subject. Regards _____________________________________ Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School Bldg 149, 13th street, Charlestown, MA 02129

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Re: [Freesurfer] IndexError: list index out of range
by Maksimovskiy, Arkadiy 21 Dec '17

21 Dec '17

Hi All, I wanted to follow up on this thread because I have been getting a similar type of an error. Here is the info from the terminal: [arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] amaksimovskiy% aparcstats2table --subjects SILVA033 SILVA035 SILVA039 SILVA040 SILVA041 SILVA044 SILVA046 SILVA048 SILVA049 SILVA050 SILVA051 SILVA052 --hemi rh --meas volume --parc aparc --tablefile Desikan_rh_volume_table.Dec17.txt SUBJECTS_DIR : /Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits Parsing the .stats files Traceback (most recent call last): File "/Applications/freesurfer/bin/aparcstats2table", line 376, in <module> parc_measure_map = parsed.parse(options.meas) File "/Applications/freesurfer/bin/fsutils.py", line 215, in parse val = float(strlist[self.measure_column_map[measure]]) IndexError: list index out of range Note: If I run the “aparcstats2table” command separately for each file, an error does not occur (i.e. when I do “aparcstats2table asegstats2table -s SILVA033 --meas volume --stats wmparc.stats --tablefile Subcortical_WM_Volume1.Dec17_SILVA033.txt). I would love to hear if anyone has solutions for this. Thanks, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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dcmunpack
by Keiko McCreary 21 Dec '17

21 Dec '17

Hi There, Could someone tell me how long approximately dcmunpack should take? (I have 243 files and it has been "interrogating" now for 2 hours. Thank you! Keiko -- J. Keiko McCreary, PhD Postdoctoral Fellow SARTAN-AD Clinical Research Coordinator (Lethbridge Site) Canadian Centre for Behavioural Neuroscience University of Lethbridge Office: EP 1218 Phone: 403-394-3985 Cell: 403-393-0181 keiko.mccreary2(a)uleth.ca or @gmail.com

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Optseq Help
by Dirks, Bryce Ronald Alan 21 Dec '17

21 Dec '17

Hello, I am trying to create the optseq for a cognitive flexibility experiment we are conducting. It consists of 10 flexibility, 10 control, and 10 fixation trials. The flexibility and control trials are 12 seconds long. Our TR= 2s. We want to ensure our trial onsets are not time-locked to our TR. We are also unsure how long our response window should be given our rather long trial duration (12s). The code below is what I have made to try to do this and I keep getting that the schedules were ill-conditioned. Any information on how to resolve this error is appreciated! ./optseq2 --ntp 180 --tr 2 --psdwin 0 30 1 --ev flexibility 12 10 --ev control 12 10 --nsearch 10000 --nkeep 3 --o cFIST_10trials8s_Run1 Thank you, Bryce Dirks Research Associate Brain Connectivity and Cognition Laboratory Department of Psychology University of Miami Website: http://www.psy.miami.edu/bccl/ Phone: (305)284-3286

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Re: [Freesurfer] Hippocampal segmentation flips on the left side
by Iglesias Gonzalez, Eugenio 21 Dec '17

21 Dec '17

Very weird! Can you please send us the log files? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 21/12/2017, 17:51, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Lauri Tuominen" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of ljtuom(a)utu.fi> wrote: Dear Freesurfers, When I run the freesurfer 6.0 recon-all -hippocampal-subfields-T1 command to segment a MNI152 template, the resulting segmentation of the left hippocampus is flipped in right-left dimension. Otherwise the right hippocampus and the subcortical segmentations in the aseg-file look fine. I encountered a similar problem when I segmented a 7T scan. Would you know what might cause this how to fix it? Thanks so much for your advice! Lauri Tuominen

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Hippocampal segmentation flips on the left side
by Lauri Tuominen 21 Dec '17

21 Dec '17

Dear Freesurfers, When I run the freesurfer 6.0 recon-all -hippocampal-subfields-T1 command to segment a MNI152 template, the resulting segmentation of the left hippocampus is flipped in right-left dimension. Otherwise the right hippocampus and the subcortical segmentations in the aseg-file look fine. I encountered a similar problem when I segmented a 7T scan. Would you know what might cause this how to fix it? Thanks so much for your advice! Lauri Tuominen

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Recon-all killed during mris_fix_topology
by Daan de Jong 21 Dec '17

21 Dec '17

Hello FreeSurfer Developers, I'm attempting to run recon-all on a MPRAGE acquisition (just a single one), and for many subjects the process gets killed during the mris_fix_topology script. An example of the message I get: CORRECTING DEFECT 5 (vertices=22062, convex hull=4299, v0=4005) Killed Linux RAD-MEMORYCL Recon-all –s PINxxx_t0 exited with ERRORS at Tue Dec 19 07:14:34 CET 2017 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I’ve attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: CentOS release 6.8 (Final) 3) uname -a: Linux RAD-MEMORYCL004 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 21:57:07 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached With kind regards, *Daan de Jong, MSc*

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