Freesurfer February 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
199 discussions

FreeSurfer Lab seeks Research Assistant
by Allison Player 08 Feb '12

08 Feb '12

Please forward to anyone you think may be interested: Position involves working in a fast-paced Computational Neuroimaging Lab. The lab develops and maintains software for MR image analysis and works primarily in a UNIX environment. The lab is also responsible for several in vivo and ex vivo (human) MRI projects. We are seeking a Research Assistant to take on several job responsibilities from a list of potential responsibilities. The Research Assistant would be responsible for work on several projects. One major project would be assisting with the scanning for the Vietnam Era Twin Study of Aging (VETSA), a large-scale research project on cognitive aging in twins. Scans are early Wednesday and Saturday mornings, every week, March through August and every other week (or less) for the rest of the year. In addition to the above, the Research Assistant would help with high resolution ex vivo scanning projects on the 3 and 7 Tesla MRI scanners. Candidate must be willing to work evenings and weekends to perform some of the experiments, including being on call during designated weekends to respond to technical problems. Candidate must also be comfortable interacting with brain tissue. Other potential projects may include: -Quality checking in vivo MRI data that has been processed by the FreeSurfer software package and manually fixing errors. -Debugging and testing specific elements of FreeSurfer. For this and the above project, the candidate must be comfortable with computers and beta testing software. -Assisting with histological processing: sectioning, mounting, histochemical and immunocytochemical staining. -Manually labeling in vivo and ex vivo MRI images. Candidate should be able to work independently, show initiative, be confident in making decisions, able to multitask, not easily stressed, and one who is not easily discouraged by failed experiments but enjoys a challenge. Candidate should have a Bachelor's or Master's Degree. Relevant backgrounds would be Neuroscience, Psychology, Engineering, Computer Science, and/or Biology. A responsible individual with a flexible schedule is required. Experience in imaging and knowledge of UNIX and scripting is preferred. Knowledge of neuroanatomy or programming is a plus. Position offers great opportunities to work with prominent scientists, people from a variety of fields, a famous Research Center, a great and fun team, opportunities to publish, as well as guidance and support for future career choices. Please send resumes and cover letters to Allison Stevens at this email address.

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mri_compile_edits
by Michael Harms 08 Feb '12

08 Feb '12

Hi Nick, Why does mri_compile_edits (-showedits flag) report edits to brainmask.mgz (both in the edits.mgz volume and its text output) if no manual edits were actually performed -- i.e, if brainmask.mgz and brainmask.auto.mgz are identical? thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Defects in freesurfer output
by Rashmi Singh 08 Feb '12

08 Feb '12

Hello, I am getting defects in the volume output of freesurfer with respect to the pial surface and whilte-matter surface boundary. I am wanting to measure the cortical thickness after running recon_all. I was inspecting the pial and white surface using tkmedit and I noticed (volume data view using tkmedit) that in most of my subjects the freesurfer has included non-cortical matter (ex: cerebellar regions) as cortical matter and have excluded several white matter voxels. I use brainmask volume loaded as main volume and white matter volume loaded as aux volume to inspect the final pial and white surfaces. These defects are more clearly visible when I get the subcortical segmentation in on mode to be viewed or when I am viewing the pial/white surface boundaries in the images where brainmask is loaded as main volume with T1.mgz as the aux volume and subcortical segmantation in on mode. Interestingly such defects were found in same regions across the subject and are present in more than one section. If what I am seeing are defects, this would be require too much editing. I am very new to freeSurfer, please advise. Rashmi. ________________________________ 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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Re: [Freesurfer] Reposting: Clusters by Multiple comparison
by Douglas N Greve 08 Feb '12

08 Feb '12

What I have listed as fa.nii.gz should be the same file that you passed to mri_glmfit with the --y option. doug Antonella Kis wrote: > Dear Doug, > > THANKS SO MUCH for your help. My last questions is: I suppose the --i > fa.nii.gz is an input file. What should be my input in thi scase if > for each subject I have different fa values and gor the mri_glmfit I > used the GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz which is the > concanetated masked file resampled to the CVS space. Should I use this > file or what exactly for the fa.nii.gz? > > Also will mri_volcluster but it will give the correct clusters if I am > not mentioning the --reg option? > > MAny thanks and have a great day! > Antonella > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Wednesday, February 8, 2012 1:50 PM > *Subject:* Re: Reposting: Clusters by Multiple comparison > > Oh, ok, I remember this now. Yes, you can use your mri_volcluster > command below the clusters. To get the table, run > mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i fa.nii.gz > --avgtwf fa.avg.dat --sum permcsd.sig.cluster.summary > > The fa.avg.dat will have a table of data. Each row will be a subject, > each column a cluster (matching that found in permcsd.sig.cluster.summary) > > doug > > > Antonella Kis wrote: > > > > > > Hi Doug, > > > > Thank you very much for your help. I attached the log file. I can > get the clusters summary if I run the mri_volcluster but it will give > the correct clusters if I am not mentioning the --reg option? > > Also, when I am visualizing my clusters using tkmedit: > > > > tkmedit cvs_avg35 norm.mgz \ > > -ov > /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh > \ > > -seg > /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh > \ > > > /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut > \ > > -fthresh 0.2 -fmax 1 > > > > I can read the functional value for each cluster. What exactly this > value represents? Is my FA value or -log10(p)? > > > > How can I get my FA values within each cluster in a table? > > > > > > > > Thank you so much. > > Antonella > > > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>> > > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Wednesday, February 8, 2012 11:37 AM > > *Subject:* Re: Reposting: Clusters by Multiple comparison > > > > Hi Antonella, the right way to do it is to figure out what is going > wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you > send the log file? Should be permcsd.mri_glmfit-sim.log. If you need > to run it for debugging purposes, you can run it with 10 iterations > (change permcsd to permcsdtmp so you don't overwrite what is there). > This should produce all the files, so if something is not there, it > should be easy to track down why. > > doug > > > > Antonella Kis wrote: > > > > > > > > > Dear Doug, > > > > > > When I run the: > > > mri_glmfit-sim \ > > > --glmdir GroupAnalysis_pos.glmdir \ > > > --sim perm 10000 3 permcsd \ > > > --sim-sign pos \ > > > --cwpvalthresh .05 > > > > > > I am not getting my clusters file permcsd.sig.cluster.mgh with > the clusters summary so as you recommended I am running the > > > > > > mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask > Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig > Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum > Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn > Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 > --seg cvs_avg35 norm.mgz --csdpdf > Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd > Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig > Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh > > > > > > > > > My question is: it is OK if I am not mentioning any registration > or what should I input under --reg while I running the mri_volcluster > if my for DTI preprocessing I used the dt_recon which computes for > each subject an fa.nii and register.dat using the Talairach > registration and later I registered all my subjects on the CVS space? > > > > > > Thank you. > > > AK > > > > > > > > > > -- Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > > > 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. > > > > > > > > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Question about ?h.sulc and ?h.curv
by Jing Ming 08 Feb '12

08 Feb '12

Hi surfers: I have a two questions. 1) how does freesurfer calculate ?h.sulc file and ?h.curv. Are they calculated after gray/white/csf segmentation? Are they calculate based on gray/white boundary? So, difference between ?h.sulc or ?h.curv will directly come from white matter change, right? 2) what's the difference between ?h.sulc and ?h.curv? In terms of sulcal structure, does ?h.sulc indicate sulcal depth and ?h.curv somehow indicate sulcal width? To me, from the display, ?h.sulc seems a smoothed version of ?h.curv. From some reference, I know .sulc is also called average convexity, so is the convexity for each vertex averaged within a small region or is it averaged through the whole hemisphere brain surface? Thanks much for your help! BestJing

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Re: [Freesurfer] Reposting: Clusters by Multiple comparison
by Antonella Kis 08 Feb '12

08 Feb '12

Hi Doug, Thank you very much for your help. I attached the log file. I can get the clusters summary if I run the mri_volcluster but it will give the correct clusters if I am not mentioning the --reg option? Also, when I am visualizing my clusters using tkmedit: tkmedit cvs_avg35 norm.mgz \ -ov /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh \ -seg /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh \ /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut \ -fthresh 0.2 -fmax 1 I can read the functional value for each cluster. What exactly this value represents? Is my FA value or -log10(p)? How can I get my FA values within each cluster in a table? Thank you so much. Antonella ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Wednesday, February 8, 2012 11:37 AM Subject: Re: Reposting: Clusters by Multiple comparison Hi Antonella, the right way to do it is to figure out what is going wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you send the log file? Should be permcsd.mri_glmfit-sim.log. If you need to run it for debugging purposes, you can run it with 10 iterations (change permcsd to permcsdtmp so you don't overwrite what is there). This should produce all the files, so if something is not there, it should be easy to track down why. doug Antonella Kis wrote: > > > Dear Doug, > > When I run the: > mri_glmfit-sim \ > --glmdir GroupAnalysis_pos.glmdir \ > --sim perm 10000 3 permcsd \ > --sim-sign pos \ > --cwpvalthresh .05 > > I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters summary so as you recommended I am running the > > mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh > > > My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space? > > Thank you. > AK > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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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Longitudinal Processing, can I salvage cross-sectional edits during processing stream? Mark
by Mark Fletcher 08 Feb '12

08 Feb '12

Dear Everyone, First of all, I have been very impressed by the functionality and abilities of FreeSurfer. I have a question about the longitudinal processing stream. I have two sets of MRI at two different time points for elderly individuals. Before version 5.1 came out, I ran the first years data through the recon-all step while using version 5.0. Additionally, I made a substantial amount of corrections to many brain regions that I am hoping to not redo (with the number of subjects in my study it will take well over a month or two to re-do this). I collected my second years worth of data after 5.1 came out, and ran the recon-all on all of these subjects using version 5.1 of FreeSurfer. Similarly, I have already made corrections to this set of data as well. My ultimate goal is to now use the longitudinal processing stream. I think I understand the process, however, I am wondering if I need to re-do all of my corrections, or if I can salvage my corrections made from previous versions. I am a little concerned about what the -clean flag might do (will it eliminate my corrections?) Furthermore, while looking at your suggestions of editing errors, it says that you can "save time" because some changes only need to be made to the base. However, in my case, I think re-doing all of the edits will actually cost me much more time. I am willing to scrap all of my work if this is necessary, but I am wondering if there is a work-around. Sincerely, Mark

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Clusters by Multiple comparison
by Antonella Kis 08 Feb '12

08 Feb '12

Dear Doug, When I run the: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 10000 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters summary so as you recommended I am running the mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space? Thank you. AK

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Visualising the FA group analysis results
by Antonella Kis 08 Feb '12

08 Feb '12

Dear Experts, I completed my FA group analysis and I expect my FA to be larger in controls versus patients (based on the uncorrected results). I corrected by multiple comparisons using: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1000 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 so I have my: permcsd.sig.cluster.nii – map of significance of clusters permcsd.sig.ocn.nii and grf.th3.pos.sig.ocn.lut – segmentation of significant clusters permcsd.sig.cluster.summary – text file of cluster table (clusters, sizes, MNI305 XYZ, and their significances) 1) How can I visualize my results more exactly how I can visualize my uncorrected and corrected results. 2) How I can output in a table the FA values corresponding to each cluster? 3) If use tkmedit is the Functional value given me the FA values while moving the cursor or this Functional value represents something else in the case I plot: tkmedit cvs_avg35 norm.mgz \ -ov /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh \ -seg /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh \ /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut \ -fthresh 0.2 -fmax 1 Thank you very much, Antonella

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volume smoothing
by Klein, Holger 08 Feb '12

08 Feb '12

Dear Freesurfers, Having used mri_label2vol I received a suitable volume that was slightly unsmooth unfortunately. I was looking for a proper command to ameliorate the smoothness of my volume but could not find a solution. Could anyone give me an advice to cope with that problem? Any help is greatly appreciated, Thanks in advance, Holger

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Freesurfer February 2012