Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

Re: [Freesurfer] Longitudinal freesurfer analysis question
by Martin Reuter 11 Nov '13

11 Nov '13

Hi Salil, please send questions to the free surfer mailing list. If you used the longitudinal stream for processing the etiv should be the same in all time points. It is computed in the 'base' = within subject template once for the entire series. It seems that you did not run your images through the longitudinal stream if your etiv is different across time points. For longitudinal processing see here: http://freesurfer.net/fswiki/LongitudinalProcessing Bes,t Martin On Nov 10, 2013, at 3:37 PM, Salil Soman <salsoman(a)stanford.edu> wrote: > Dear Dr. Reuter, > > I have performed freesurfer 5.3 with hippo subfields Analysis on patients that have 2 consecutive scans (pre and post surgery). I have generated Segstats statistics for each individual time point. I have noticed the etiv is different on all of the cases for each time point (scan 1 is different from 2). This has led me to worry that it may not be legitimate to perform analyses of changes in volumes of structures by computing differences in values between time points). I am writing to inquire if you were familiar with /had an opinion regarding this matter. > > Best wishes, > > Salil Soman, MD, MS > Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory > Fellow - Palo Alto War Related Illness and Injury Study Center > WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System > --------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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request
by pietro de rossi 11 Nov '13

11 Nov '13

Dear Freesurfers, I am working on the segmentation of mdeft structural images (Siemens Allegra 3T-acquired) of schizophrenia patients. I had troubles editing temporal regions (especially superior temporal gyrus) by adding control points. After re-running the image in the pipeline (autorecon2-cp) the problem on the STG was solved but the pial and white matter boundaries in the lower temporal regions were completely messed up. Could anyone take a look and tell me if the image is editable? I would like to upload the pre and post editing folders so that an expert can give me an opinion. Is this the correct link to upload files and folders? https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Sorry to bother you all but this would be extremely helpful given that I experienced a similar problem in several subjects of this sample. Thanks in advance, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com<http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

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Error in Config File
by Cherise R. Chin Fatt 11 Nov '13

11 Nov '13

Hello: I am trying to run two subjects using Tracula. I have created a config file, and getting the following error: set: Variable name must begin with a letter. ERROR: must specify as many DWI dicoms as subjects I have tried to debug and can't seem to find the source of this problem. My config file is as follows: setenv SUBJECTS_DIR /FreeSurfer_Reconstruction/All_Recons set dtroot = /FreeSurfer_Reconstruction/DTI_Raw set subjlist = (PID0001 \ PID0002) set dcmroot = /FreeSurfer_Reconstruction/DTI_Raw set dcmlist = (PID0001/orig/000031.DCM \ PID0002/orig/00001.dcm) Any help would be appreciated. Thank you, Cherise.

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Strange segmentation - what is going on?
by Erik Lindberg 11 Nov '13

11 Nov '13

Dear Freesufer experts, I attached an image that display really odd segmentation of a brain - I do not understand why this is happening - I got it in quite a lot of these from my last run of Freesufer - any suggestion on what is going on? Thanks Olof

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Etiv difference in difference in same patient
by Salil Soman 10 Nov '13

10 Nov '13

Hi, My understanding of etiv is that it is derived from the registration of a brain to atlas space and not actually derived from the freesurfer segmentation. I have a set of patients imaged at 2 time points that all have different etiv values between the first and second scan that are statistically significant. As there was no change in their skulls between scans, I am having difficulty understanding how this is possible. Can anyone suggest what I may be doing wrong? Best wishes, Salil

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acquisition in 1 session vs 2 sessions
by Daniel Ferreira 09 Nov '13

09 Nov '13

Dear experts, We are designing a study including a long MR protocol: 1) Localizer 2) Cal 3) T1-FSPGR 4) FLAIR 3D 5) DTI 1 6) DTI 2 7) fMRI Due to patients characteristics we were thinking on splitting the acquisition in two different sessions (session 1: sequences 1, 2, 3, 4; session 2: sequences 1, 2, 5, 6, 7). Do you think we should do the same for the healthy controls or we can scan them in just one single session? I wonder how system session-related artifacts could differentially affect the two kinds of protocol (spitted vs. single). I also wonder how FreeSurfer processing can be affected by this issues. Thanks a lot. Daniel Ferreira

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Re: [Freesurfer] -autorecon 3 error: error reading surf/lh.sphere
by Adam Mezher 08 Nov '13

08 Nov '13

Absolutely, sorry about that, the group is now cc'd. the ls -l says: -rw-rw-r-- 1 vhasfcwui cind 0 Nov 6 15:57 lh.sphere so it has 0 size to it, and I can't open it in tksurfer -bash-3.2$ tksurfer PPMI_290_S_3829m12_i395612 lh sphere Using Freesurfer version 5.1. subject is PPMI_290_S_3829m12_i395612 hemi is lh surface is sphere surfer: current subjects dir: /cind/00/PPMI/Freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /cind/07/PPMI/Freesurfer/subjects checking for nofix files in 'sphere' Reading image info (/cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612) Reading /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/mri/orig.mgz surfer: Reading header info from /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/mri/orig.mgz ERROR: reading /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/surf/lh.sphere Read 0 bytes, expected 1 Perhaps I should first try deleting the file and rerun as you recommended? Thanks, Adam On Fri, Nov 8, 2013 at 2:36 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Adam > > can you cc the list on your replies so that others can answer? What does > ls -l say about the sphere? Can you open it in tksurfer? Maybe the > partition filled at some point when it was being written but things opened > up later? You might just deleted the lh.sphere file and run > > recon-all -make all -s <subject> > > cheers > > Bruce > > > On Fri, 8 Nov 2013, Adam Mezher wrote: > > Hi Bruce, >> >> Yes I checked and the partition is not full, there should be ample space >> available. >> Do you have any other ideas? I've never come across this error before. >> >> Thanks, >> -Adam >> >> >> Filesystem Size Used Avail Use% Mounted on >> cosf:/cind/07 2.3T 2.0T 167G 93% /cind/07 >> >> On Fri, Nov 8, 2013 at 2:22 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Adam >> >> can you check to make sure that the partition isn't full? >> >> Bruce >> On Fri, 8 Nov 2013, Adam Mezher wrote: >> >> Hi FreeSurfer experts, >> >> I am repeatedly running into an autorecon3 error (see below). >> Any ideas how to fix >> this? It appears that the software is having an issue reading >> /surf/lh.sphere and >> immediately exits afterward. >> >> Thank you, >> Adam >> >> >> >> Adam Mezher >> >> Staff Research Associate II >> >> Center for Imaging of Neurodegenerative Diseases >> >> San Francisco VA Medical Center >> >> 4150 Clement St. (114M) >> >> San Francisco, CA 94121 >> >> Tel: 415-221-4810 Ext. 4629 >> >> Fax: 415-668-2864 >> >> >> >> >> >> using smoothwm curvature for final alignment >> $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ >> reading surface from ../surf/lh.sphere... >> mris_register: could not read surface file ../surf/lh.sphere >> ERROR: reading ../surf/lh.sphere >> Read 0 bytes, expected 1 >> Linux aldebaran 2.6.18-194.17.4.el5 #1 SMP Mon Oct 25 >> 15:50:53 EDT 2010 x86_64 x86_64 >> x86_64 GNU/Linux >> >> recon-all -s PPMI_290_S_3829m12_i395612 exited with ERRORS at >> Wed Nov 6 15:57:07 PST >> 2013 >> >> >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine >> at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >>

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-autorecon 3 error: error reading surf/lh.sphere
by Adam Mezher 08 Nov '13

08 Nov '13

Hi FreeSurfer experts, I am repeatedly running into an autorecon3 error (see below). Any ideas how to fix this? It appears that the software is having an issue reading /surf/lh.sphere and immediately exits afterward. Thank you, Adam *Adam Mezher* Staff Research Associate II Center for Imaging of Neurodegenerative Diseases San Francisco VA Medical Center 4150 Clement St. (114M) San Francisco, CA 94121 Tel: 415-221-4810 Ext. 4629 Fax: 415-668-2864 using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... mris_register: could not read surface file ../surf/lh.sphere ERROR: reading ../surf/lh.sphere Read 0 bytes, expected 1 Linux aldebaran 2.6.18-194.17.4.el5 #1 SMP Mon Oct 25 15:50:53 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PPMI_290_S_3829m12_i395612 exited with ERRORS at Wed Nov 6 15:57:07 PST 2013

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sulci depth in table
by Tara Ann Miskovich 08 Nov '13

08 Nov '13

Hello, I am extracting sulci depth using the following mri_segstats --annot ${subject} lh aparc --sum lh.sulc.sum --i surf/lh.sulc Do you know how I could put this into aparcstats2table? Thank you, Tara

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glm_fit --prune
by celine＠nmr.mgh.harvard.edu 08 Nov '13

08 Nov '13

Hi, When using glm_fit with an input volume that has many voxels with a 0 value (due to a previous thresholding for quality reasons), and the voxel removes might be distributed randomly across our population, is there a way not to take into account those voxels in the glm_fit model? I saw the --pune flag, but I am not sure if it is the one to use. Thanks Celine

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