Freesurfer July 2012

freesurfer@nmr.mgh.harvard.edu

128 participants
194 discussions

significant variation in Hippocampal volume in between scans of same subject
by Rashmi Singh 27 Sep '12

27 Sep '12

Hello, I am finding differences in hippocampus voulme of same subject when scanned at different times . Our study requires our subjects to be scanned 3-4 times (T0-T3) within a period of 1 month. We have performed MRI Scanning on all our subjects with same sequence using 3T GE scanner. Please suggest the reason behind this difference and how would I go about correcting it. For example following are the hippocampal values for two subjects ( A and AA ) calculated by freesurfer from different scans. Surprisingly for these two subjects T3 and T2 Hipp-values for A and AA respectively that are differing from the other timepoints are same. Left-Hippocampus Right-Hippocampus A.T0 3537 3632 A.T1 3629 3796 A.T2 3536 3782 A.T3 3096 3671 AA.T1 4245 4667 AA.T2 3096 3671 AA.T3 4341 4491 ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

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qdec.table.dat file
by Fidel Vila 10 Sep '12

10 Sep '12

Hi Freesurfer experts, A newbie question regarding working with QDEC. When I try to upload the qdec.table.dat file (attached) an error messages pops up "Error loading the data table". To the best of my knowledge I've followed the guidelines on the tutorial in terms of formatting. What would be your suggestions to troubleshoot this? Thanks! Fidel

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missing ROI when using mri_label2vol to transfer ic2.tri
by Leon 05 Sep '12

05 Sep '12

Hi, folks when I transferred the annotation file obtained using mri_make_face_parcellation based on ic2 (162 labels) to a volume file using mri_label2vol, I found that one ROI patch was missing in the volume file (see attached). I searched archives and the closest thread I could found is that somebody reported an ROI with the last index was missing in the mgz file after they were transferred from the annotation file to the volume file. Could someone help on this? If this happens to be a bug, is there any other strategy that will allow me to get a GM/WM ribbon without a hole on it? Many thanks in advance Leon

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Subcortical segmentations
by Jordan Pierce 08 Aug '12

08 Aug '12

Hi, I have a question about subcortical segmentations: there are a lot of places across subjects where the thalamus label seems to include white matter (images attached), am I right to think that this needs to corrected and is there any reason the program might do this so often? Thanks, Jordan Pierce

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longitudinal stats
by Rajagopalan, Venkateswaran 31 Jul '12

31 Jul '12

Hi All, I am trying to do cortical thickness analysis on a single subject's longitudinal data. I am attaching the design and group.diff.mtx could any one tell me whether they are correct. Thanks venkat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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DODS Overlay
by Ian Carroll 31 Jul '12

31 Jul '12

Hello, If I were to run a DODS -- say, an F-test looking for group differences and interactions in thickness among drug users vs non- users, dependents vs abusers, and drug use in the last month vs no use in the last month -- how would I visualize the results? I assume there's no intelligible way to make an overlay out of interactions, unless you look at the F-test output one contrast at a time (e.g., what areas show a significant interaction in thickness between dependents vs abusers and use in the last month?). Take care, Ian Carroll

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Re: [Freesurfer] Optic chiasm resisting edits
by Peter McNally 31 Jul '12

31 Jul '12

Whoops forgot to select reply all... Yes I am erasing the chiasm using tkmedit--I'll rerun autorecon-wm now and send the recon-all.log results when they finish (probably) tomorrow. Thank you, Peter On Tue, Jul 31, 2012 at 2:34 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > can you cc the list on these emails? And try rerunning autorecon2-wm and > send us the recon-all.log results? You are erasing the chiasm using > tkmedit, aren't you? > > > On Tue, 31 Jul 2012, Peter McNally wrote: > > The edits do not appear to be reflected in the filled.mgz (the chiasm is >> still present on the filled.mgz volume). The same is true for ?h.orig, and >> they are even worse than normal on ?h.orig.nofix. >> >> On Tue, Jul 31, 2012 at 2:14 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> > >> wrote: >> hmmm. And are the edits reflected in the filled.mgz? Is the >> chiasm gone? How about in the ?h.orig and ?h.orig.nofix? >> On Tue, 31 Jul 2012, Peter McNally wrote: >> >> Hi Bruce, >> >> Thank you for your speedy response. Yes, I ran >> -autorecon2-wm -autorecon3. >> >> Best, >> Peter >> >> On Tue, Jul 31, 2012 at 2:03 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Peter >> what did you run after editing it out of the >> wm.mgz? You should >> be running -autorecon2-wm -autorecon3 >> >> cheers >> Bruce >> >> >> On Tue, 31 Jul 2012, Peter McNally wrote: >> >> Dear FreeSurfer Experts, >> >> I am using Freesurfer version 5.1 over >> at the >> University of Pennsylvania, >> and I have been running into issues with >> the optic >> chiasm. Despite having >> edited it out on both the brainmask.mgz >> and wm.mgz >> volumes, FreeSurfer has >> been insisting that it be included as a >> surface on >> multiple participants. >> Does anyone know a way to resolve this? >> Thank you >> very much for your time. >> >> Best, >> Peter McNally >> >> >> PS: I have included an example as an >> attachment >> (.pdf) >> >> >> >> >> >> >> 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<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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Re: [Freesurfer] Recon-all -qcache curvature error & recon-all make -all
by Gibbard, Clare 31 Jul '12

31 Jul '12

Hi Bruce, Thanks, I've attached the end of the recon-all.log file for one of the subjects (the whole thing was too large). This is what I get when I run recon-all -version: $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ When I try to run recon-all -s subject_no -make all I don't think anything comes up in the log. I get this in the terminal window: clare@clare-OptiPlex-990:~/subjects$ recon-all -s subject_20 -make all Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Subject 'subject_20': make all make: Nothing to be done for `all'. clare@clare-OptiPlex-990:~/subjects$ Let me know if you need anything else. Thank you. Best wishes, Clare ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: 25 July 2012 14:44 To: Gibbard, Clare Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all -qcache curvature error & recon-all make -all Hi Clare can you send us the screen output and also what version you are running? thanks Bruce On Wed, 25 Jul 2012, Gibbard, Clare wrote: > Hello, > > I have run several scans using recon-all -all -subjid subject_no -expert > expert.opts where my expert.opts file changes the parameters for the > mri_normalize step (this works well in my scans). I then had to edit a few > of the scans by adding in more white matter and a few control points. I > re-ran them to incorporate the edits using recon-all -s subject_no -make all > -xopts-use. This worked well. > > I then ran recon-all -s subject_no -qcache ready for doing a group > analysis. I got an error reading the curvature file in those subjects I had > edited. I can see from the mailing list that others have had this error > previously and ran recon-all -s subject_no -make all to fix it. I tried > this, but I got a message saying that there was nothing to be done for all. > > Are you able to advise me on what I can try now? Do I need to go back a > step? > > Thank you very much, > Clare > > 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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Re: [Freesurfer] Label to ROI volume
by mmoayedi＠uhnres.utoronto.ca 31 Jul '12

31 Jul '12

Dear Dr. Fischl, Thank you for your respone. What would the --reg and the --temp be in this case? Massieh > ---------------- Original message ------------------ >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >To: mmoayedi(a)uhnres.utoronto.ca-> >cc: freesurfer(a)nmr.mgh.harvard.edu-> >Subject: Re: [Freesurfer] Label to ROI volume > > try mri_label2vol (assuming by 'ROI' you mean a 3D volume) > > On Mon, 30 Jul 2012, mmoayedi(a)uhnres.utoronto.ca wrote: > > > > > Dear FS Experts, > > > > I have run recon-all on my subjects. I'm looking to convert the V1 and > various BA labels to ROIs in 3D anatomical space (orig.mgz). How would I > convert my freesufer label files to ROIs. Thank you! > > > > Massieh Moayedi > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > 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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Optic chiasm resisting edits
by Peter McNally 31 Jul '12

31 Jul '12

Dear FreeSurfer Experts, I am using Freesurfer version 5.1 over at the University of Pennsylvania, and I have been running into issues with the optic chiasm. Despite having edited it out on both the brainmask.mgz and wm.mgz volumes, FreeSurfer has been insisting that it be included as a surface on multiple participants. Does anyone know a way to resolve this? Thank you very much for your time. Best, Peter McNally PS: I have included an example as an attachment (.pdf)

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Freesurfer July 2012