Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

Re: [Freesurfer] ROI analyses
by Douglas N Greve 07 May '13

07 May '13

On 05/07/2013 05:21 AM, Tudor Popescu wrote: > Hi Doug, > I was just wondering whether you received my last email, with > follow-ups on your answers. Sorry for the multitude of questions - as > ever, I really appreciate the help! > Best wishes, > Tudor > > On 4 May 2013 20:31, Tudor Popescu <tudor3(a)gmail.com > <mailto:tudor3@gmail.com>> wrote: > > Sorry Doug, wasn't sure whether you'd seen my reply > Tudor > > > ---------- Forwarded message ---------- > From: *Tudor Popescu* <tudor3(a)gmail.com <mailto:tudor3@gmail.com>> > Date: 2 May 2013 21:54 > Subject: Re: [Freesurfer] ROI analyses > To: freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Thanks Doug! If I may follow up: > > > 3) (I can't see whether there's a tutorial for this, as the > main FS > > site seems to be down at the moment) How can a group > comparison of CT > > be done inside a given ROI, and in what ways can the ROI be > specified? > > I guess the command line version of QDEC would produce, in > this case, > > the same contrasts as QDEC, but within the ROI as opposed to > the whole > > brain > You mean you want to do an exploratory analysis within a mask > of an ROI > or that you want to average the CT scan within the ROI and do > a group > analysis of the ROI values? If the former, you can use > mri_glmfit with > the -label or -mask option. If the latter, you can create a > table with > asegstats2table then run mri_glmfit with --table > > 3') Is it the case that mri_glmfit with mask=brainmask.mgz is > equivalent to doing a whole-brain analysis in QDEC? > QDEC is only doing surface-based analysis. brainmask.mgz is a volume. But in principle the idea is similar. > > > 3'') I didn't find, on the mri_glmfit help page, how masks can be > formed out of one of the atlas structures, e.g. > "lh_S_intrapariet_and_P_trans "... The --table argument is also > not present anywhere on that page.. > You can run mri_annotation2label to convert an annotation to label, then pass the label to glmfit. > > > 3''') Would it not be a/parc/stats2table rather than > a/seg/stats2table, if the ROI in question was cortical and not > subcortical? Is the difference between what FS calls > "segmentation" and "parcellation" just terminology, i.e. the > former delineates subcortical structures and the latter delineates > cortical structures? Or does it imply anything else? > Whether you use one or the other depends on whether you generate the individual table with mris_anatomical_stats (aparcstats2table) or mri_segstats (asegstats2table) > > > 4) How do the results of these two different types of ROI group > > analyses differ, and is one of them more "correct" than the > other: > > A) running the command prompt version of QDEC within the > confines > > of a certain atlas-defined ROI, and looking at the resulting > > statistical map (clusters), as per question 3; > > B) extracting the CT values for that ROI for all > subjects using > > aparcstats2table, and doing t-tests to look for a group > difference. > Oops, looks like these are the two I mentioned from #3 above. > The first > is an exploratory analysis in which the groups are compared on a > vertex-by-vertex basis. If there is a subset of vertices that are > different between the groups, it may show up in the exploratory > analysis. However, the effect may be small at each vertex and > averaging > over the vertices may improve your power (unless the effect is > only at a > few vertices). One is not more correct than the other, just > testing > different hypotheses. > > 4') Can the second option (averaging the CT values within the ROI) > not also be done by taking the values from the table into SPSS and > simply doing an independent samples t-test? Is that not equivalent > to what mri_glmfit would do in this case? > Yes, it should be the same. > > > And one more question: > 5) Can the statistical map in QDEC be built using a lower, > uncorrected p value (e.g. 0.0001) instead of an FDR-corrected test > value? > Yes, just set the threshold (FDR is off by default). doug > > > Thanks!! > Tudor > > doug > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <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> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 > <mailto:Freesurfer@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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Re: [Freesurfer] Issues with Cluster generation
by Douglas N Greve 07 May '13

07 May '13

Hi Joshua, there are several issues. First, you are using a threshold of p<.0001 which is pretty severe. It works for the tutorial, but you need to understand what this threshold is and pick one appropriate for your data. Second, you are only doing 5 iterations. You need to be doing something like 10000. If you are doing a whole cortex analysis, you can use the cached table instead of doing a simulation (with --qache). Running your own simulation will take a long time. The smoothing level is a little high, I usually run at 10 or 15. There's nothing wrong, it is just a little high. doug On 05/05/2013 03:39 AM, Joshua deSouza wrote: > Hi Doug, > > The image has undergone fwhm 20 smoothing. > > The final glmdir file is given in the attachments. RC.txt was the > contrast name and folder in which the cluster correction files are kept. > > The glmdir creation command line : mri_glmfir --y lh.thomasR.20.mgh > --fsgd R.txt dods --C RC.txt --surf fsaverage lh --cortex --glmdir > lh.thomasR.glmdir > > The glmfit-sim command line is : mri_glmfit-sim --glmdir > lh.thomasR.glmdir --sim mc-z 5 4 mc-z.negative --sim-sign neg > --cwpvalthresh 0.999 --overwrite > > The command line to view the image is : tksurfer fsaverage lh inflated > -annot lh.thomasR.glmdir/RC.txt/mz-z.negative.sig.ocn.annot fthresh 1 > -curv -gray > > The version of freesufrer i'm using is 1.379.2.17 > > Thank you helping me out with this. > > > On Sat, May 4, 2013 at 12:12 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Can you send the command line and terminal output and the version > of FS > you are using? > doug > On 05/03/2013 09:01 AM, Joshua deSouza wrote: > > Hello all, > > > > I am facing a problem whereby after running GLMfit and cluserwise > > correction for multiple comparisons using the monte-carlo method, I > > was unable to generate any clusters. I do have significant images > > produced for the glmfit. > > > > All procedures were done according to the tutorial to match the > > effects under FSGD. > > > > There are no clusters available even when I set the cwpvalthresh to > > .999 which is supposed to show all clusters. What is the cluster > > generation dependent upon? As my glmfit does show significant areas. > > > > Please advise > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto:Freesurfer@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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Segmentation fault (core dumped) again in the BETA version
by martina.andellini＠fastwebnet.it 07 May '13

07 May '13

Hi Freesurfer experts, I've got Ubuntu version 13.04 installed on my computer, and after I saw the post : "http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html" I d ecide to install the BETA version freesurfer-Linux-centos6_x86_64-stable-pub-v5. 3.0-BETA.tar.gz as adviced. I still run into the same error when I run mri_nu_correct.mni and tkmedit: Segmentation fault (core dumped) ERROR: converting to minc and =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... : Can anyone please advice on that? thanks a lot Martina

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Neuroimaging Research Technician
by Emily Lindemer 07 May '13

07 May '13

* * * * ** *A Neuroimaging Research Technician position is available in the VA Boston Healthcare System (VABHS) Neuroimaging Research for Veterans (NeRVe) Center. * * The Neuroimaging Research Technician will provide technical support for image preprocessing and analysis (using programs such as FSL and FreeSurfer), maintenance and development of in-house custom processing codes (script writing in unix/linux, matlab, etc), and assist staff members in the conduct of neuroimaging research as well as administrative tasks related to the Center. This includes developing expertise and training other investigators with the operation of current MRI hardware (scanner console, goggles, headphones, BioPac system, etc) and software for data processing and analysis. Additional responsibilities will include management of online documentation and center resources. Technical skills and familiarity with Linix/Unix, Matlab, and imaging software packages such as FSL and FreeSurfer is beneficial. Applicants should have a minimum of a Bachelor’s degree, with a background in Neuroscience, Computer Science, Engineering, Math or Physics. A two year commitment is required. Must be a U.S. citizen. Interested candidates should email a cover letter, resume, and contact information for two professional references to Emily Lindemer at emily.lindemer(a)va.gov . *

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NFS v4 on CentOS 5.4 or Red Hat 6.2
by Garikoitz Lerma-Usabiaga 07 May '13

07 May '13

Hi FS experts, we have changed our file systems to NFS v4 and we found that FS cannot write to it (I mean, FS installed in an app server and subjects in the file system is not working). Last new I have is that FS in CentOS could read but not write and in Red Hat could not write or read. Is it a known problem? Is it something going on with FS or the problem is in our end? (the rest of the programs are working fine: FSL, Matlab...) Many thanks, Gari

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Qdec analysis for only particular regions of interest?
by Klara Mareckova 07 May '13

07 May '13

Hello, I'm new to Freesurfer and I was wondering whether anybody could tell me what steps I need to do in Freesurfer in order to conduct the following analysis? I would like to know which sex differences in cortical thickness (subjects 12-18 years old) are present in the 12 year olds already. I've used qdec to calculate the main effect of sex in a) all participants (12-18) and b) in 12 year olds. Is there a way how to mask the 12-year olds' results with the whole group so that I can calculate which of the whole-group main effects are present before the age of 13? Thanks a lot for any suggestions, Klara

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Fwd: Re: repeat: trouble loading nifti files
by Akshay 07 May '13

07 May '13

mri_convert path-to-nifti file mask.mgz --resample_type nearest -cs 256 On 5/7/13 2:55 PM, Bruce Fischl wrote: > can you send me the full mri_convert command line that is run? > On Tue, 7 May 2013, Akshay wrote: > >> Hi Bruce >> >> Please find the file attached >> >> Best, >> >> Akshay >> >> >> On 5/7/13 2:40 PM, Bruce Fischl wrote: >>> Hi Akshay >>> >>> is you send us that file we'll take a look. >>> >>> cheers >>> Bruce >>> On Tue, 7 May 2013, Akshay wrote: >>> >>>> Hi All, >>>> >>>> I am re-posting this question since there was no response to my >>>> previous >>>> attempt. >>>> >>>> I have a problem conforming certain nifti files, the following is the >>>> log when i try to convert them, >>>> >>>> reading from >>>> /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137_S_1041_MR_MIDAS_Whole_Brain_Mask_Br_20120723235935683_S22310_I317755.nii... >>>> INFO: using NIfTI-1 qform >>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >>>> i_ras = (0, -4.99113e-10, -1) >>>> j_ras = (-4.99113e-10, -1, 4.99113e-10) >>>> k_ras = (-1, 4.99113e-10, 0) >>>> WARNING >>>> ==================++++++++++++++++++++++++======================================= >>>> The physical sizes are (281.25 mm, 280.14 mm, 216.72 mm), which cannot >>>> fit in 256^3 mm^3 volume. >>>> The resulting volume will have 282 slices. >>>> If you find problems, please let us know >>>> (freesurfer(a)nmr.mgh.harvard.edu) >>>> ==================================================++++++++++++++++++++++++=============== >>>> >>>> Original Data has (1.09862, 1.09429, 1.20399) mm size and (256, 256, >>>> 180) voxels. >>>> Data is conformed to 1 mm size and 282 voxels for all directions >>>> Reslicing using nearest >>>> >>>> >>>> This is understood, however I want them to be conformed to 256^3 >>>> mm. If >>>> I use -cs 256 flag, it does resample the image to 256^3mm but the >>>> image >>>> is blank. >>>> >>>> Is there something wrong I am doing? How do I conform these files >>>> to 256^3mm? >>>> >>>> Any help will be greatly appreciated. >>>> >>>> Best, >>>> >>>> Akshay >>>> >>>> >>>> _______________________________________________ >>>> 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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TrackVis "either end" command
by Chu, Catherine,M.D. 07 May '13

07 May '13

Dear Freesurfer/TrackVis experts, I am using the following command in a batchfile to identify tracks counts between dozens of preset ROIs. track_vis DATAPATHtob0.trk -roi DATAPATHTOROI1.nii -roi2 DATAPATHTOROI2.nii -o PATHTOOUTPUT.trk > OUTPUT.txt -nr', i, j, i, j, i, j Is there a line command I can use so that the tracks identified follow the rule "either end" in the ROIs instead of the default "any part"? Thank you! Cat

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repeat: trouble loading nifti files
by Akshay 07 May '13

07 May '13

Hi All, I am re-posting this question since there was no response to my previous attempt. I have a problem conforming certain nifti files, the following is the log when i try to convert them, reading from /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137_S_1041_MR_MIDAS_Whole_Brain_Mask_Br_20120723235935683_S22310_I317755.nii... INFO: using NIfTI-1 qform TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -4.99113e-10, -1) j_ras = (-4.99113e-10, -1, 4.99113e-10) k_ras = (-1, 4.99113e-10, 0) WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (281.25 mm, 280.14 mm, 216.72 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 282 slices. If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) ==================================================++++++++++++++++++++++++=============== Original Data has (1.09862, 1.09429, 1.20399) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 282 voxels for all directions Reslicing using nearest This is understood, however I want them to be conformed to 256^3 mm. If I use -cs 256 flag, it does resample the image to 256^3mm but the image is blank. Is there something wrong I am doing? How do I conform these files to 256^3mm? Any help will be greatly appreciated. Best, Akshay

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BBregister issue during autorecon3 with T2pial option (5.2.0 with updated beta binaries)
by Todd Thompson 06 May '13

06 May '13

Hi, all. I'm trying to refine my pial surfaces with a T2 (or, in this case, t2*) image and I'm running into an error inside bbregister/fslregister. I'm running the command: recon-all -s gf04 -3T -autorecon3 -T2pial -T2 /mindhive/gablab/fluid/Analysis/Nipype/flash/gf04/tissue_parameters/T2star.mgz and the recon process makes it to the point of #@# Refine Pial Surfs w/ T2/FLAIR when it runs: bbregister --s gf04 --mov /mindhive/gablab/fluid/Data/gf04/mri/orig/T2raw.mgz --lta /mindhive/gablab/fluid/Data/gf04/mri/transforms/T2raw.lta --init-fsl --T2 bbregister does some initial processing, then calls fslregister, like so: fslregister --s gf04 --mov /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/template.nii --reg /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/fslregister --dof 6 --fsvol brainmask which immediately crashes with: /mindhive/gablab/fluid/Data/gf04 mri_convert ERROR: could not determine file for /mindhive/gablab/fluid/Data/gf04/mri/ERROR: /mindhive/gablab/fluid/Data/gf04/mri/transforms/tmp.bbregister.23921/fslregister/refvol.fslregister.nii And so on. running the fslregister command manually and changing "brainmask" to "brainmask.mgz" seems to fix the problem (after manually creating/filling the appropriate tmp directory, of course). Any thoughts? Thanks!

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