Freesurfer August 2012

freesurfer@nmr.mgh.harvard.edu

110 participants
170 discussions

Whole Brain Volume
by Christopher McCarthy 23 Aug '12

23 Aug '12

Hello All, We are looking into alternative measures for whole brain volume to use for covarying, and the previous topic mentioned mris_volume as a possibility but it isn't located on the top of the aseg file. Has it been moved? Chris McCarthy

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Re: [Freesurfer] Tracula question
by Anastasia Yendiki 23 Aug '12

23 Aug '12

Can you please check that the x-y-z dimensions of the bedpostx output files are the same as the dimensions of the DWIs? On Thu, 23 Aug 2012, Natalia Sánchez wrote: > Thanks for your response!Attached are the requested files > > The error occurs here are shown on my terminal: > Loading b-values from/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmri/bv > als > Loading gradients from/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmri/bv > ecs > Segmentation fault > Darwin dhcp-165-124-9-141.phystherapy.northwestern.edu 10.8.0 Darwin Kernel > Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; > root:xnu-1504.15.3~1/RELEASE_I386 i386 > > > -- Natalia Sánchez > PhD Candidate > Departments of Biomedical Engineering & > Physical Therapy and Human Movement Sciences Northwestern University > 645 North Michigan Ave, Suite 1100 > Chicago, IL 60611 > > > > > On Thu, Aug 23, 2012 at 1:48 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Natalia - I'd need to see at which point in the processing > the error occurs, since this is a very generic error message. > Can you please include your trac-all.log and dmrirc? > > Thanks, > a.y > > On Thu, 23 Aug 2012, Natalia Sánchez wrote: > > Hi Anastasia!I finally made tracula -prep work > without errors, using the 1mm > T1 MNI template (i tried using the 2mm one but the > vertices for registering > white matter came out as NaN). However, I was not > able to get bedpost to > work. After looking at other posts on the FS > archive, I think the reason why > -bedp does not work is because of my FSL version. I > tried running bedpost on > FSL and then just copying those files on my > dmri.bedpost folder and using > those files for reconstructing the white matter > tracts. However, I get a > "Segmentation Fault" error. Do you have any idea > what this error may mean? > > My dpath folder is empty and I my trac-all.log file > has no errors related to > -path > > Thanks! > > > > -- Natalia Sánchez > PhD Candidate > Departments of Biomedical Engineering & > Physical Therapy and Human Movement Sciences > Northwestern University > 645 North Michigan Ave, Suite 1100 > Chicago, IL 60611 > > > > > On Fri, Aug 10, 2012 at 5:05 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Natalia - This is an error that will occur > if lowb_brain_mask > does not exist. The command that generates > lowb_brain_mask is > "bet" - can you find that line in the log file > and run it > directly on the command line and see if you > get an error? > > On a separate note, have you opted to use a > DWI mask instead of > an anatomical mask by setting usemaskanat = 0? > If not, then it > may be that it's trying to use the DWI mask > b/c it can't find > the anatomicals, in which case I'd check if > SUBJECTS_DIR has > been set properly and a freesurfer recon of > the same subject > exists there. But this is a separate > issue than the DWI mask not being generated. > > Hope this helps, > a.y > > On Fri, 10 Aug 2012, Natalia Sánchez wrote: > > The required files were not generated. > > the error occurs at > > rh.slft_PP_roi2.flt.nii.gz--bmask/Users/Natalia/Desktop/freesurfer/subjects > /Justin/cJD/dlabel/mni/low > b_brain > _mask.flt.nii.gz--fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/d > mri/mni/dtifit_F > A.fl > t.nii.gz --ncpts 5 --trunc --debug > ERROR: fio_pushd: > > /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni > ERROR: Must specify brain mask volume for > output subject > > does the brain mask have to be input manually > in the > configuration file, or > is this part of the pre-processing? since I > set the bet > thr to 0.23 in the > config file i thought the brain mask was also > created > during the > preprocessing stage. Attached is my log file. > > I am familiar with FSL but I am using Free > surfer since i > think automating > the entire process, including tracking is a > great > advantage, but I'm just > starting to get the hang of it > > Thanks! > > > > -- Natalia Sánchez > PhD Candidate > Departments of Biomedical Engineering & > Physical Therapy and Human Movement > Sciences > Northwestern University > 645 North Michigan Ave, Suite 1100 > Chicago, IL 60611 > > > > > On Fri, Aug 10, 2012 at 4:28 PM, Anastasia > Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > dtifit_FA.fl > t.nii.gz > > > > > > > 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] Tracula question
by Anastasia Yendiki 23 Aug '12

23 Aug '12

Hi Natalia - I'd need to see at which point in the processing the error occurs, since this is a very generic error message. Can you please include your trac-all.log and dmrirc? Thanks, a.y On Thu, 23 Aug 2012, Natalia Sánchez wrote: > Hi Anastasia!I finally made tracula -prep work without errors, using the 1mm > T1 MNI template (i tried using the 2mm one but the vertices for registering > white matter came out as NaN). However, I was not able to get bedpost to > work. After looking at other posts on the FS archive, I think the reason why > -bedp does not work is because of my FSL version. I tried running bedpost on > FSL and then just copying those files on my dmri.bedpost folder and using > those files for reconstructing the white matter tracts. However, I get a > "Segmentation Fault" error. Do you have any idea what this error may mean? > > My dpath folder is empty and I my trac-all.log file has no errors related to > -path > > Thanks! > > > > -- Natalia Sánchez > PhD Candidate > Departments of Biomedical Engineering & > Physical Therapy and Human Movement Sciences Northwestern University > 645 North Michigan Ave, Suite 1100 > Chicago, IL 60611 > > > > > On Fri, Aug 10, 2012 at 5:05 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Natalia - This is an error that will occur if lowb_brain_mask > does not exist. The command that generates lowb_brain_mask is > "bet" - can you find that line in the log file and run it > directly on the command line and see if you get an error? > > On a separate note, have you opted to use a DWI mask instead of > an anatomical mask by setting usemaskanat = 0? If not, then it > may be that it's trying to use the DWI mask b/c it can't find > the anatomicals, in which case I'd check if SUBJECTS_DIR has > been set properly and a freesurfer recon of the same subject > exists there. But this is a separate > issue than the DWI mask not being generated. > > Hope this helps, > a.y > > On Fri, 10 Aug 2012, Natalia Sánchez wrote: > > The required files were not generated. > > the error occurs at > > rh.slft_PP_roi2.flt.nii.gz--bmask/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/low > b_brain > _mask.flt.nii.gz--fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_F > A.fl > t.nii.gz --ncpts 5 --trunc --debug > ERROR: fio_pushd: > /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni > ERROR: Must specify brain mask volume for output subject > > does the brain mask have to be input manually in the > configuration file, or > is this part of the pre-processing? since I set the bet > thr to 0.23 in the > config file i thought the brain mask was also created > during the > preprocessing stage. Attached is my log file. > > I am familiar with FSL but I am using Free surfer since i > think automating > the entire process, including tracking is a great > advantage, but I'm just > starting to get the hang of it > > Thanks! > > > > -- Natalia Sánchez > PhD Candidate > Departments of Biomedical Engineering & > Physical Therapy and Human Movement Sciences > Northwestern University > 645 North Michigan Ave, Suite 1100 > Chicago, IL 60611 > > > > > On Fri, Aug 10, 2012 at 4:28 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > dtifit_FA.fl > t.nii.gz > > > > > > > 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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qdec generate stats data tables
by Nathan Hutcheson 23 Aug '12

23 Aug '12

I am trying to use the "generate stats data tables" feature in qdec but am getting the error message below. So based on the error message I know that the trouble subject is SZ0020 and I looked in his file and found the attached aseg.stats file, which looks okay. I reven tried rerunning the segstats using recon-all -s SZ0020TS/ -segstats. Any ideas? asegstats2table --common-segs --meas volume --tablefile /Applications/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects SZ_0020 SZ_0030 SZ_0033 SZ_0045 SZ_0049 SZ_0050 SZ_0058 SZ_0067 SZ_0006 SZ_0037 SZ_0038 SZ_0040 SZ_0048 SZ_0051 SZ_0053 SZ_0054 SZ_0059 SZ_0060 SZ_0062 SZ_0065 SZ_0069 SZ_0071 SZ_0072 SUBJECTS_DIR : /Applications/freesurfer/subjects Parsing the .stats files ERROR: The stats file /Applications/freesurfer/subjects/*SZ_0020*/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Take care, Nathan Hutcheson Graduate Research Assistant 501 Sparks Center 1748 7th Ave South Birmingham, AL 35233

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FDR Correction of NHP Surface Data
by Clark Fisher 23 Aug '12

23 Aug '12

Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark

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Re: [Freesurfer] Help removing marking from DICOM/.nii files
by Douglas N Greve 22 Aug '12

22 Aug '12

Hi Alex, there's no way to "erase" it in a way that you can recover the underlying signal. I'm surprised that such small things are causing the talairach to crash. If the writing is always the same value and that value does not appear in other parts of the image, you might be able to replace the value with values of nearby voxels. Let me know if you need some instructions on this. doug On 08/22/2012 02:08 PM, Alexandra Tanner wrote: > Hi Doug, > > I'm currently working with 4-6 year old clinical pediatric non-Siemens > DICOM files that I'm unpacking and preprocessing in freesurfer. So far > we've been able to unpack the DICOMS to .nii format and successfully begin > the autorecon process for our first few subjects. We've noticed, when > looking at the raw scans for some of our subjects, however, there is > writing (probably information from the scan console) included in the > images, and in some slices, slightly overlapping with the outer edge of > the skull/brain. When attempting to run the autorecon1 on these scans, the > command terminates during the talairach transform. We're thinking, since > we don't have this issue with all of our subjects, the writing may be what > is causing the problem. > > I'm wondering if you know of any way to remove the writing from the images > (I tried seeing if I could erase the lettering in tkmedit but it seems it > can't be erased manually). Attached is a screenshot of a coronal slice > with the writing. Any suggestions would be greatly appreciated! > > Thanks, > Alex > -- 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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label2vol with yeo annotation - dropping region#17
by Anisha Keshavan 22 Aug '12

22 Aug '12

Hello - I'm having trouble using label2vol with the 17 network yeo annotation -- mri_label2vol --annot lh.Yeo2011_17Networks_N1000.SAD_P05.annot --o outfile.nii.gz --hemi lh --subject SAD_P05 --temp /mindhive/xnat/surfaces/sad/SAD_P05/mri/orig.mgz --identity The annotation was created by mri_surf2surf (fsaverage5 --> SAD_P05's surface) and it does have region17. Any idea what's happening? Thanks, Anisha

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Edits to aparc+aseg.mgz
by Sarosh, Cyrus 22 Aug '12

22 Aug '12

Hello FreeSurfer Users, I looked for a possible solution to my problem in the Mail Archive and found this article referring to almost the exact same problem I am having: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314.html. Basically, pieces of the subarachnoid space/pia mater/arachnoid/dura mater/skull are being segmented as the cortex in certain slices and this occurs when it is physically adjacent to the gray matter. Besides this point everything else seems to be running smooth. In the related article I found that this may be caused by the MR parameters so I will give you the acquisition information that I know. The acquisitions are SPGRs, taken on either a GE 3T or 1.5T and the resolution is 1mm isotropic. Any solutions besides going through each series slice by slice and making corrections would be greatly appreciated. Thanks, Cyrus ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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two Post Doc positions at the Karolinska Institute
by Ivanka Savic-Berglund 22 Aug '12

22 Aug '12

Please, observe the announcement of two new post doctoral positions in NeuroImaging and behavior at the Karolinska Institute in Stockholm - https://ki.netrecruiter.se/what:job/jobID:13820/where:4/ -https://ki.netrecruiter.se/what:job/jobID:13880/where:4/ Ivanka Savic MD, PhD ivanka.savic-berglund(a)ki.se Associate Professor, senior lecturer in Neurology Dept of Women´s and Children´s Health Karolinska Institute Scheeles väg 3 Karolinska Institute 171 77 Stockholm Ph +46852480000 Mo +46709380738

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cortical surface area related measures
by Gregory Kirk 22 Aug '12

22 Aug '12

Hi folks, I wanted to make sure i have everything straight w.r.t. the surface area measures. as i see there are 4 ways implemented ( somewhere ) to do cortical surface area analysis. 1. areal expansion 2. Local Gyrification Index 3. direct vertex based true surface area glm, Winkler AM et. al 4. roi based, i.e. based on the surface areas of the parcellation units in lh.aparc.a2009s.stats etc. 1. recent pub, Lisa T. Eyler et. al used the areal expansion method. was this done exactly as would be achived by using the area tab on qdec and setting up a glm ? Dale published surface area specifying some details of implementation but i was not sure if this was exactly what is implemented in qdec ? 2. LGI seems to me this is the ratio of two areas, that of the hull to the area inscribed by projecting the border of the hull onto the grey/white surface. In an e-mail Nick said LGI is a curvature based measure and that confused me a bit. gyrification is of course related to curvature but it seems the quantities actually calculated here are ratios of areas, which gives local info on surface area differences. 3. the winkler stuff is i think not publicly available yet at this time ? 4. straightforward enough not withstanding ICV corrections, etc. any words of clarification before i start trying some analysis on my group ? thank you Greg

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Freesurfer August 2012