Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

Morphological operations on surface labels
by Michael Waskom 09 Jun '13

09 Jun '13

Hi, Are there any utilities for performing basic morphological operations on surface-based label files buried somewhere within Freesurfer? Specifically I am hoping to perform a closing. Thanks! mw

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Announcement: ESMRMB Lectures on MR: Educational on Resting State fMRI Vienna – September 2-4, 2013
by leemon albert 09 Jun '13

09 Jun '13

ESMRMB Lectures on MR: Educational on Resting State fMRI Vienna – September 2-4, 2013 After the big success of last year’s workshop in Magdeburg, we are proud to announce the 2013 Resting State Educational Workshop taking place in Vienna, September 2-4. The 3-day educational workshop, organized together with the ESMRMB – Lectures on MR Series, will feature the most relevant topics related to resting state imaging, including physiology, data analysis, and applications. The target audience, researchers with existing knowledge on fMRI with an interest to broaden and substantiate their knowledge on resting state fMRI, will get to experience in-depth lectures and hands-on analysis sessions by international experts in the field. Faculty: Christian Beckmann (Donders, NL) Fahmeed Hyder (Yale University, US) Catie Chang (NIH, US) Peter Fransson (Karolinska, Sweden) Mika Rubinov (Cambridge, UK) Sepideh Sadaghiani (Berkeley, US) Lucina Uddin (Stanford, US) Vesa Kiviniemi (Oulu, Finnland) Bharat Biswal (UMDNJ, US) Christian Windischberger (Vienna, Aus) Ilya Veer (Charité, Germany) Martin Walter (Magdeburg, Germany) For more information on the course program and speakers, or to simply register, please visit www.restingstate.com or www.esmrmb.org. The registration fee for PhD students and physicians in training is € 240 for ESMRMB members and € 335 for non-members, which includes access to the workshop, a course syllabus, full catering of lunches and coffee breaks, and a welcome dinner. After the workshop, a 2-day scientific mountain event will complement the course and provide the opportunity to present own work and get together with peers and colleagues. We are looking forward to see you in Vienna! Christian Windischberger Martin Walter Ilya Veer

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subfield algorithm and subject intensity differences
by Joshua Lee 08 Jun '13

08 Jun '13

I'm trying to understand Leemput's subfield algorithm better as implemented in Freesurfer. Does the algorithm make use of intensity differences in the internal hippocampal lamina from the subject's T1 image to warp meshes and assign subfield probabilities? Or does it depend only on outward boundaries of the hippocampus and probability priors to determine the inner boundaries between CAs and dentate gyrus? - Josh

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Re: [Freesurfer] Cortical thickness
by Joshua deSouza 08 Jun '13

08 Jun '13

Hello Doug, Each individuals subject data has already been smoothed by 5 10 15 20 and 25 through the qache function during the initial processing. I'm a little confused now. I thought that the mri_preproc would use the non-smoothed values of the subjects and create an mgh file. After which I smooth the mgh file and then use mri_glmfit to analyse it according to the contrasts. If the above is not the case and the subject data has already been smoothed, then what should I do if I wish my final mgh file to have a smoothing value of 15 before doing a glmfit on it? Thank you, Joshua On Wed, Jun 5, 2013 at 12:40 AM, Joshua deSouza <desouzajoshua00(a)gmail.com>wrote: > Hello Doug, > > Each individuals subject data has already been smoothed by 5 10 15 20 and > 25 through the qache function during the initial processing. > > I'm a little confused now. I thought that the mri_preproc would use the > non-smoothed values of the subjects and create an mgh file. After which I > smooth the mgh file and then use mri_glmfit to analyse it according to the > contrasts. > > If the above is not the case and the subject data has already been > smoothed, then what should I do if I wish my final mgh file to have a > smoothing value of 15 before doing a glmfit on it? > > Thank you, > > Joshua > > On Mon, Jun 3, 2013 at 11:13 PM, Douglas Greve <greve(a)nmr.mgh.harvard.edu>wrote: > >> >> Hi Joshua, when you add --fwhm 15 to the command line you are instructing >> mri_glmfit to smooth by 15mm. Is this what you want? Or is the data >> already smoothed? >> doug >> >> >> >> On 6/3/13 12:26 AM, Joshua deSouza wrote: >> >> Hi Doug, >> >> The command line is mri_glmfit --y lh.t.15.mgh --fsgd t.txt dods --C >> t1.txt --surface fsaverage lh --cortex --fwhm 15 --glmdir lh.t.15.glmdir >> >> I am doing a whole hemisphere analysis and am measuring cortical >> thickness. I do not have my own mask but I have doubts about the mask that >> has been produced because from previous studies, there has been significant >> thinning in the area around the hippocampus and parts of it are being left >> out in the mask, such as the para-hippocampal region. >> >> Regards >> >> Joshua >> >> On Mon, Jun 3, 2013 at 10:54 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu >> > wrote: >> >>> >>> The residual FWHM is measured from the data itself. You apply a certain >>> amount of smoothing, but there is already some smoothness to the data, so >>> the final fwhm is a combination of what is already there and what you >>> apply. A fwhm of 47 is huge and may indicate that something is wrong. What >>> is the input? cortical thickness? Are you using your own mask or is this a >>> whole hemisphere analysis? >>> >>> doug >>> >>> >>> >>> >>> >>> >>> On 6/2/13 10:29 PM, Joshua deSouza wrote: >>> >>> Hello Doug, >>> >>> Thank you for your quick replies to my queries. Really appreciate it. >>> >>> I have found the files containing the cortical thickness values. Thank >>> you. I assume that the order in which they follow are based on the fsgd >>> file and the cluster annotation numbers. >>> >>> I was just slightly confused about the residual fwhm. I have already >>> done a smoothing of 15 on the file and have recieved a residual value of >>> 47, which I assume is extremely large. Since I'm finding out values for the >>> entire cortex I cannot do a glmfit-sim as there are no fwhm cache values of >>> 47. Could you please tell me what the residual values mean? What do you >>> recommend I do? Is there anything I can read up on to find out more about >>> this? (Please pardon my questions if they seem a little trivial) >>> >>> Thank you >>> >>> Joshua >>> >>> On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve < >>> greve(a)nmr.mgh.harvard.edu> wrote: >>> >>>> >>>> This file is always created by mri_glmfit-sim. It might be named >>>> something different depending on your parameters (should always end in >>>> y.ocn.dat) >>>> doug >>>> >>>> >>>> On 6/2/13 3:57 AM, Joshua deSouza wrote: >>>> >>>> Hi Doug, >>>> >>>> This file that your saying, will be created after glmfit-sim is done >>>> using the cache function and a threshold of 1.3 and absolute ,with y being >>>> the fsgd file? Am I understanding this correctly? >>>> >>>> Thank you >>>> >>>> Joshua >>>> >>>> On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve < >>>> greve(a)nmr.mgh.harvard.edu> wrote: >>>> >>>>> There should be a file called something like cache.th13.abs.y.ocn.dat. >>>>> This will have a column for each cluster and a row for each subject. >>>>> The >>>>> value in the row will be the input for each subject. >>>>> doug >>>>> >>>>> On 05/30/2013 11:21 PM, Joshua deSouza wrote: >>>>> > Hello everyone, >>>>> > >>>>> > Please pardon my rather simple question >>>>> > >>>>> > I have done a GLM fit anlysis and have obtained a file sig.mgh alonf >>>>> > with a few others after the analysis.As I know, I do not have to >>>>> > create ROIs in order to do this. I also understand that doing a >>>>> > multiple comparison analysis just compares the regions of importance >>>>> > and evaluates them giving the most resilient cluster depending on the >>>>> > threshold. So, this does not give a thickness estimate. I would like >>>>> > to know how do I get the cortical thickness values from the results? >>>>> > If so, can I do it after glmfit? >>>>> > >>>>> > And thanks Doug for your help in the other questions that I had prior >>>>> > to this! >>>>> > >>>>> > Thank you >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > Freesurfer mailing list >>>>> > Freesurfer(a)nmr.mgh.harvard.edu >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> -- >>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> Outgoing: >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> 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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Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
by Douglas N Greve 07 Jun '13

07 Jun '13

Hi Pablo, please respond to the list and not to us directly. Please just cut and paste the text of the error into the email. thanks doug On 06/06/2013 12:30 PM, pablo najt wrote: > Thank you for your quick response. I have re run the installation but > I get the following erros with _tkmedit bert orig.mgz_ and _tksurfer > bert rh pial_ commands. > Please see attach for the detailed errors. > Best, > Pablo > > > > Date: Thu, 6 Jun 2013 12:01:22 -0400 > > From: greve(a)nmr.mgh.harvard.edu > > To: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed} > > > > what command is not found? > > On 06/06/2013 11:58 AM, pablo najt wrote: > > > Hello I have a question regarding the installation/running FreeSurfer. > > > I have just completed the installation and got the confirmation that > > > Free surfer was installed. Please see snapshot. > > > However when I follow the steps for testing (*MailScanner has > detected > > > a possible fraud attempt from "connect.yale.edu" claiming to be* > > > https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer > > > > <https://connect.yale.edu/owa/14.3.123.3/scripts/premium/redir.aspx?C=Alh1Yj…>), > > > > I always get "command not found". I was wondering if you would be > able > > > to help me. > > > Thanks, > > > Pablo > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > 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. > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Hypointense lesions
by Fotiadis, Panagiotis 07 Jun '13

07 Jun '13

Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos

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mri_convert
by Ray, Siddharth 07 Jun '13

07 Jun '13

Hi free-surfer folks, I have some subjects with L-R header flipped in nifti's. Is it possible to flip the header using mri_convert so that I can have the right orientation information for subjects. Please let me know. Thanks, -Siddharth

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FS-FAST - ERROR: mapping surfaces
by preciado＠nmr.mgh.harvard.edu 07 Jun '13

07 Jun '13

I am having an issue when running the preprocess script in fs-fast. It failed once and I tried something and ran the script again and it failed the same way. The command I ran is: preproc-sess -s subj007 -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Below is the part where the error appears to occur, but the full log is attached. Any help would be appreciated. -Ronny 1/1 subj007 1/1 subj007 008 lh --------- Fri Jun 7 10:50:50 EDT 2013 mri_vol2surf --mov /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz --reg /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/masks/brain.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz srcreg = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.cortex.label Reading surface /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 19272 Reading source surface registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.sphere.reg Done loading source registration surface surf2surf_nnfr(): Vals and Reg dimension mismatch nVals = 157755, nReg 157894 Reading target registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (subj007 -> fsaverage) ERROR: mapping surfaces

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R: Re: R: Re: mris resample: Command not found. This error is permanent after new patch download
by stdp82＠virgilio.it 07 Jun '13

07 Jun '13

Ok, now I think that I have downloaded the correct file. I try to rerun trac-all -prep and at the end I'll send you a feedback. Thanks, Stefano ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 7-giu-2013 18.18 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: mris resample: Command not found. This error is permanent after new patch download I dont know why your getting a file named "unknown". If you click this link you should be able to download a file called "mris_resample": ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/ Download it and place it in $FREESURFER_HOME/bin (Usually Applications/freesurfer/bin on Macs). Then make it executable by typing "chmod +x Applications/freesurfer/bin/mris_resample" on the command line. -Zeke If you go this this link On 06/07/2013 12:09 PM, stdp82(a)virgilio.it wrote: > Hi Zeke, thank you very much. > > I have download a file that named "unknown". > > I should rename it as "mris_resample"? > > > Stefano > > ----Messaggio originale---- > Da: zkaufman(a)nmr.mgh.harvard.edu > Data: 7-giu-2013 18.02 > A: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] mris resample: Command not found. This error is > permanent after new patch download > > Stefano, step 4 should be: > > "chmod +x $FREESURFER_HOME/bin/mris_resample" > > When you do an "ls -l" in the $FREESURFER_HOME/bin directory, you need > to see the to see the x's next to mris_resample just like you do with > all the other files in that directory. > > -Zeke > > > On 06/07/2013 11:49 AM, stdp82(a)virgilio.it wrote: > > Hi list, > > > > during trac-all -prep I have this error: > > > > MRISregister() return, current seed 0 > > writing registered surface to > > > /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... > > expanding nbhd size to 1 > > mris_resample: Command not found. > > Darwin iMac > > > > I have performed my analysis by the following steps (as recommended by > > Zeke and Lilla): > > > > 1. download "unKnow" file (7.6 MB) at > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample > > 2. put file in $FREESURFER/bin/ > > 4. chmod +x ~/mris_resample as recommended by Daniel (in the first test > > I did not use this command) > > 5. start trac-all -prep > > 6. ERROR (in inter-reg step) > > > > What's happen? > > > > Thank you very much, > > > > > > Stefano > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > 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. > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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R: Re: mris resample: Command not found. This error is permanent after new patch download
by stdp82＠virgilio.it 07 Jun '13

07 Jun '13

Hi Zeke, thank you very much. I have download a file that named "unknown". I should rename it as "mris_resample"? Stefano ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 7-giu-2013 18.02 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] mris resample: Command not found. This error is permanent after new patch download Stefano, step 4 should be: "chmod +x $FREESURFER_HOME/bin/mris_resample" When you do an "ls -l" in the $FREESURFER_HOME/bin directory, you need to see the to see the x's next to mris_resample just like you do with all the other files in that directory. -Zeke On 06/07/2013 11:49 AM, stdp82(a)virgilio.it wrote: > Hi list, > > during trac-all -prep I have this error: > > MRISregister() return, current seed 0 > writing registered surface to > /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... > expanding nbhd size to 1 > mris_resample: Command not found. > Darwin iMac > > I have performed my analysis by the following steps (as recommended by > Zeke and Lilla): > > 1. download "unKnow" file (7.6 MB) at > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample > 2. put file in $FREESURFER/bin/ > 4. chmod +x ~/mris_resample as recommended by Daniel (in the first test > I did not use this command) > 5. start trac-all -prep > 6. ERROR (in inter-reg step) > > What's happen? > > Thank you very much, > > > Stefano > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ 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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Freesurfer June 2013