Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Freesurfer and Google Drive
by Arindam Chatterjee 21 Jan '16

21 Jan '16

Hello Freesurfer experts, Does anyone have experience running freesurfer on a mac, pointing to images stored on Google Drive? Due to space issues on disk, I was trying to take that approach, but when I run recon-all pointing to the image stack, I get errors - and it says "For more details, see the log file". Where is the log file stored that I can look at? Sorry - newbie questions... Ankita

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Hippocampal subfields
by Alan Francis 21 Jan '16

21 Jan '16

Hi Eugenio: Hope all is well. I have a question. I have run the HSF algorithm on 32 brains and they ran smoothly without problems. I used only T1 scans. I did not have T2s. Now to extract the data, do I need to run the following: *<analysisID>.FSspace.mgz*: the additional scan, rigidly registered to the T1 data. *[lr]h.hippoSfLabels-<T1>-<analysisID>.v10.mgz*: they store the discrete segmentation volume at 0.333 mm resolution in the physical space of the FreeSurfer <https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> T1 data (and therefore of the aligned scan *<analysisID>.FSspace.mgz* as well). *[lr]h.hippoSfLabels-<T1>-<analysisID>.v10.1mm.mgz*: they store the discrete segmentation volume in the 1 mm FreeSurfer <https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> voxel space. *[lr]h.hippoSfVolumes-<T1>-<analysisID>.v10.txt*: these text files store the estimated volumes of the subfields and of the whole hippocampi. Or can I go directly to : quantifyHippocampalSubfields.sh <T1>-<analysisID> <output_file> <OPTIONAL_subject_directory> Thanks so much, best regards, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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Analyze to nii convertor
by Mahmoudi, Fariborz 21 Jan '16

21 Jan '16

Dear All, I have a set of images with analyze 75 (img/hdr) format. I want to convert them to .nii single file format. I used the following command: mri_convert -i name_of_input_file -it analyze -ot nii -o name_of_output_file But the output file has not proper nii format, When I drag the file in the MRIcro I just see a single slice with scrambled picture. It is appreciated if anybody could help me and let me know which switches I should use. Thanks, Fari ________________________________ CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies. Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy & Security page on www.henryford.com for more detailed information as well as information concerning MyChart, our new patient portal. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.

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Posterior Probability file for Hippocampal subfields segmentation
by Xinyang Feng 21 Jan '16

21 Jan '16

hi, FreeSurfer experts, I have a question about the new hippocampal subfields segmentation tool in FS 6.0. I wonder if there is an option to generate the posterior probability file like "posterior_right_CA1.mgz" generated in FS 5.3. Thanks, Xinyang

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-hippocampal-subfields-T1 problem
by Carl Anderson 21 Jan '16

21 Jan '16

Hi All, I can't seem to get V6 hipposubfields to run on my new Yosemite install. Data was processed with V5.3 under 10.6.8. Attached log..but no error occurred. Thanks for your help! Carl <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Command line: vermisii:Only_5_3 carlanderson$ recon-all -s RB_139 -hippocampal-subfields-T1 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/Only_5_3 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 carlanderson wheel 632773 Jan 21 09:41 /Applications/freesurfer/subjects/Only_5_3/RB_139/scripts/recon-all.log Darwin vermisii.mclean.harvard.edu 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Thu Jan 21 09:57:22 EST 2016 \n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 /Applications/freesurfer RB_139 /Applications/freesurfer/subjects/Only_5_3 left \n See log file: /Applications/freesurfer/subjects/Only_5_3/RB_139/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64: Warning: application is running on a locale different from the original platform locale. Registering imageDump.mgz to hippocampal mask from ASEG dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer/bin//kvlAutoCrop Reason: image not found /bin/bash: line 1: 5956 Trace/BPT trap: 5 /Applications/freesurfer/bin//kvlAutoCrop /Applications/freesurfer/subjects/Only_5_3/RB_139/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask.mgz 6 > /dev/null /Applications/freesurfer/bin//kvlAutoCrop /Applications/freesurfer/subjects/Only_5_3/RB_139/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask.mgz 6 >/dev/null: Trace/breakpoint trap /Applications/freesurfer/subjects/Only_5_3/RB_139/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 588) Error in myMRIread>myMRIread_aux (line 85) Error in myMRIread (line 56) Error in segmentSubjectT1_autoEstimateAlveusML (line 174) MATLAB:badSwitchExpression --

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segmentation fault with mri_label2vol
by Martha Shiell 21 Jan '16

21 Jan '16

Hello Freesurfer list, I have several different surface labels that I am converting into volume regions-of-interest in white matter. For 2 out of 11 participants, one of the labels will not convert. My command has worked for these two participants with all other labels that I've tried. I have no trouble viewing the label in question on the inflated surface with freeview, and no problem viewing the brain.mgz files. Ideas? Thank you, Martha Command: mri_label2vol --label d16/roi_lh_man3/lh.behav-full-sig2-transformed.label --temp ~/project_deaf_anatomy/analysis_nifti_freesurfer/d16/mri/brain.mgz --reg d16/reg/surf2conf.dat --subject d16 --hemi lh --proj abs -1 -1 0.1 --o d16/roi_lh_man3/roi_lh_man3_conf.nii.gz; done Output: Number of labels: 1 d16/roi_lh_man3/lh.behav-full-sig2-transformed.label Annot File: (null) Template Volume: /home/martha/project_deaf_anatomy/analysis_nifti_freesurfer/d16/mri/brain.mgz Outut Volume: d16/roi_lh_man3/roi_lh_man3_conf.nii.gz Registration File: d16/reg/surf2conf.dat Fill Threshold: 0 Label Vox Vol: 1 ProjType: abs ProjTypeId: 1 ProjStart: -1 ProjStop: -1 ProjDelta: 0.1 Subject: d16 Hemi: lh UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /home/martha/project_deaf_anatomy/analysis_nifti_freesurfer $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 128.000; -0.000 1.000 -0.000 128.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Loading registration from d16/reg/surf2conf.dat RegMat: -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading surface /home/martha/project_deaf_anatomy/analysis_nifti_freesurfer/d16/surf/lh.white nvertices = 114782 Reading thickness /home/martha/project_deaf_anatomy/analysis_nifti_freesurfer/d16/surf/lh.thickness nlabels = 1 Allocating Hit Volume (16777216) voxels Loading d16/roi_lh_man3/lh.behav-full-sig2-transformed.label Segmentation fault -- Martha M. Shiell, PhD

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New User - Gyrification Index question
by Arindam Chatterjee 21 Jan '16

21 Jan '16

Hello, I am a new user of the freesurfer platform. I am a high school junior conducting research on brain MRI scans and came across this wonderful platform. However I am not very sure how to proceed with my research - I am trying to find the whole brain Gyrification Index, which I did manually on a different software called ImageJ using multiple image scans of brain slices. Will freesurfer be able to analyze brain scan images and provide a whole brain GI or does it only analyse and provide local GI which is what I found through some forums? If so, are there any tutorials to learn how to do that? Do I need any other software like MatLab to find out the Gyrification Index? Thank you in advance! Ankita

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GLUT: Fatal Error in tksurfer.bin
by stdp82＠virgilio.it 20 Jan '16

20 Jan '16

Hi list, I have installed FS on my macbook (el capitain) and this error occur:tksurferGLUT: Fatal Error in tksurfer.bin: could not open displayI have look in previous mail in the forum but, although the error has been already discussed, no solution for my issue I have found.ThanksStefano

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Questions about eTIV
by Niklas Klasson 20 Jan '16

20 Jan '16

Dear FreeSurfer team, I am writing a paper about FreeSurfer's estimates of intracranial volume (eTIV), when using FreeSurfer version 5.3.0, and have two questions that I would be very grateful if you could answer. My understanding is that the alignment (from which the atlas scaling factor is calculated) of the input MR images to the MNI305 atlas is done by the “Avi Snyders 4dfp suite” (see https://surfer.nmr.mgh.harvard.edu/fswiki/talairach and https://surfer.nmr.mgh.harvard.edu/fswiki/talairach_avi) and using this suite FreeSurfer is trying to align the input images to the brain and about a two cm thick layer around the brain in the MNI305 atlas (see https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-September/008370… guess that FreeSurfer uses the function imgreg_4dfp (in the 4dfp suite, see https://searchcode.com/codesearch/view/39432481/) for the alignment with the following arguments: 1) the MNI305 atlas (as the target image), 2) a target image mask (so that the adoption/evaluation of the alignment only will be done towards the brain and the two cm thick layer around the brain), and 3) the input MR images (as the object image). My questions are: 1) Is my understanding and/or guess correct? 2) Is there any paper or manual available that you know of that describe the alignment procedure used in the 4dfp suite? Thanks in advance! Best regards, Niklas

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How to calculate the volume of subcortical structure using my own atlas?
by Tianqi Wang 20 Jan '16

20 Jan '16

Dear freesurfers, I want to calculate the volume of subcortical structure using my own atlas. But my altlas is not in the fsaverage space. In order to achieve my goal, I plan to use the mri_vol2vol command to register my atlas to the fsaverage subject and then register every subject to the fsaverage subject. At last, I want to use the mris_segstats command to calculate the volume of subcortical structure. I have two questions: 1. Is the plan above can get the right results? 2. If the plan above can get the right results, what registration matrix should I use for mri_vol2vol and how can I get the matrix? Thanks! Tianqi Wang

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