Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

Re: [Freesurfer] statistically truncate negative values
by Maya Rosen 07 Oct '13

07 Oct '13

Hi Doug, Thanks for your response. I implemented what you suggested, but I'm unclear as to what I should use as the value for --min when i use mri_binarize? At first I used 1.3, but that masked out almost all the activation. I lowered it to 0.1 just to see what would happen. That looked overall more reasonable (i.e. showing differences where there is activation and not where there are differences in deactivation). However, there are a couple of very small regions that are still showing up as having a significant difference between Condition A and Condition B, when in fact that difference is due to differences in deactivation (i.e. more deactivation in Condition B than Condition A --> shows up as A greater than B). I'd like to know what a reasonable value for the --min flag and if you have any insight into why I am still seeing some regions that show differences in deactivation. Here's what I ran: mri_binarize --i CONDITION_Avpassive/ces.nii.gz --mask CONDITION_Bvpassive/ces.nii.gz --mask-thresh 0.00001 --o ConditionAvsConditionB/point1.ces.nii --min 0.1 mri_glmfit --y ConditionAvsConditionB/ces.nii.gz --osgm --mask ConditionAvsConditionB/point1.ces.nii --glmdir point1_masked.rfx --nii --surf fsaverage lh Thanks for the help! Maya Message: 1 Date: Tue, 10 Sep 2013 15:37:01 -0400 From: Maya Rosen <mayalrosen(a)gmail.com> Subject: [Freesurfer] statistically truncate negative values To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAJzkiyGEMzm1GUke-XV0Ko5qYH3QdQAuPmZWO8Rqm-0RyTOiew(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi All, I have two conditions of interest in my GLM analysis, Condition A and Condition B. I would like to make a contrast of Condition A and Condition B that includes only those vertices that are significantly positively activated when compared to the Passive Viewing baseline. In other words, I would like to mask anything that is Passive > Condition A or Passive > Condition B and only include Condition A > Passive and Condition B > Passive when contrasting Condition A and Condition B, so as to limit my contrast to changes in *activation *in the two conditions, not *deactivation *. I see that in an older version, when isxavg-re-sess was used, there was a flag --trunc that would allow you to set the negative values to 0. If there is a way to do this in the v 5.1.0, I could then perform a second level contrast of positively activated Condition A and Positively activated condition B. Is there a way to exclude the negatively activated voxels from the Condition A vs Passive and Condition B vs Passive contrasts when looking at Condition A vs Condition B? I would like to do this statistically, not just at the map level. Thank you for your help! Maya

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LGI longitudinal data
by Tricia Merkley 04 Oct '13

04 Oct '13

Hi, Is it possible to run the LGI on data that has already been longitudinally processed? For example, when I try to run: recon-all -s subject001.long.subject001_base -localGI I get the following error: ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters: \' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists. This is using v5.1.0, and no, I'm not trying to re-run a longitudinal time point. Just the LGI. I'd appreciate any suggestions! Thanks so much, Tricia

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Error running TRACULA
by Lucia Billeci 02 Oct '13

02 Oct '13

Dear all, I am trying to apply TRACULA on my DATA (GE data) but when I run the following command: trac-all -prep -c /Users/Desktop/FreesurferData/SUBJECT1/dmrirc_subject1 after eddy current correction, I obtain this error: mv -f /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot xfmrot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.ecclog /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs printf: -.999993: expected numeric value printf: -.003594: expected numeric value printf: .000852: expected numeric value R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. fslroi /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.nii.gz /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/lowb.nii.gz 0 Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> fslroi <input> <output> <tmin> <tsize> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension. Darwin dhcp225.ifc.cnr.it 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Gio 26 Set 2013 10:12:38 CEST I attach my bvals and bvecs Could you help me? Thanks Lucia

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Re: [Freesurfer] MNI152 to 305 conversion
by Douglas N Greve 01 Oct '13

01 Oct '13

View it in tkmedit to see if it is really a problem with your vol2vol command. doug On 09/30/2013 07:33 PM, Paul Beach wrote: > No. That was just a general example of how the image looks - from a > stock google image of an FSL brain (I'm not in the lab and so cannot > put up actual images). I've been using AFNI to view them. > > > On Mon, Sep 30, 2013 at 7:23 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Is this in tkmedit? > > > On 09/30/2013 06:59 PM, Paul Beach wrote: > > Hi Doug, > > Sorry, I should have been more specific. I meant for when one > looks at the resulting transformation in a sagittal view. > > More specifically... > Instead of this: > Inline image 1 > > It looks more like this (though more like a 70degree shift > than 90): > Inline image 2 > The other views are obviously affected as well. Performing a > dataset "nudge" using afni generally "corrects" this problem, > but I'd like to prevent it from happening in the first place. > > I'm suspicious that this is occurring because I'm using > '/mni305.cor.mgz/' instead of '/mni305.2mm.nii.gz/' for the > 'mov' command. However, I don't have the latter file anywhere > in my Freesurfer directory. The former file is the closest > thing I could find. > > > Thoughts? > Paul > > > > On Mon, Sep 30, 2013 at 5:52 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > what do you mean the frontal lobe is pointing straight up? > > > > > On 09/30/2013 02:32 PM, Paul Beach wrote: > > Freesurfer experts, > > > > I'm attempting to utilize an archived e-mail's contents > to resample > > data in MNI152 to 305. > > > > The script I'm using is as follows: > > /mri_vol2vol \/ > > /--mov > > > > /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz > > \/ > > /--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz \/ > > /--reg > > $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \/ > > /--inv --o FSL_MNI305_2mm.nii.gz/ > > / > > / > > / > > / > > This series of commands is based on the following suggestion > from Doug > > in a previously archived e-mail exchange from someone > attempting > to do > > something similar: > > />> To go from mni152 to the MNI305 2mm space, use/ > > />>/ > > />> mri_vol2vol --mov mni305.2mm.nii.gz \/ > > />> --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \/ > > />> --reg > > > $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \/ > > />> --inv --o output.mni305.2mm.nii.gz/ > > />>/ > > />> This will resample MNI152_T1_2mm.nii.gz (or anything > in that > > space) to the/ > > />> mni305 2mm space./ > > > > > > However, this changing the orientation of my data - > essentially all > > images are being rotated 90degrees so the frontal lobe > is pointed > > straight up. > > > > Are there any suggestions to ameliorate this problem? > > > > Thanks! > > -- > > Paul Beach > > DO/PhD candidate - Year VI > > Michigan State University > > - College of Osteopathic Medicine > > - Neuroscience Program > > - Bozoki Lab: Neurology/Radiology > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@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> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel: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: 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> > <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> > <mailto:Freesurfer@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. > > > > > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > > > -- > 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/ > > > > > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology -- 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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overlay mni152 activation -- difference between tksurfer and freeview
by Yang, Daniel 01 Oct '13

01 Oct '13

Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat. It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold... Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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DODS slope information
by Jacobs H (NP) 01 Oct '13

01 Oct '13

Hi Freesurfers, I just looked at my cortical thickness results, in which I performed an interaction between group (2 groups) and cognition (continuous). I see regions popping up, which is great! Especially since they are related to the task. Now, I made a scatterplot of some of these vertices to get a better understanding of the effect. However, I am wondering how I can figure out if the slope within each group is significant. How can I examine that? Thanks! Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

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MNI152 to 305 conversion
by Paul Beach 30 Sep '13

30 Sep '13

Freesurfer experts, I'm attempting to utilize an archived e-mail's contents to resample data in MNI152 to 305. The script I'm using is as follows: *mri_vol2vol \* *--mov /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz \* *--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz \* *--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \* *--inv --o FSL_MNI305_2mm.nii.gz* * * * * This series of commands is based on the following suggestion from Doug in a previously archived e-mail exchange from someone attempting to do something similar: *>> To go from mni152 to the MNI305 2mm space, use* *>>* *>> mri_vol2vol --mov mni305.2mm.nii.gz \* *>> --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \* *>> --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \* *>> --inv --o output.mni305.2mm.nii.gz* *>>* *>> This will resample MNI152_T1_2mm.nii.gz (or anything in that space) to the* *>> mni305 2mm space.* However, this changing the orientation of my data - essentially all images are being rotated 90degrees so the frontal lobe is pointed straight up. Are there any suggestions to ameliorate this problem? Thanks! -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology

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Re: [Freesurfer] Effects of age on different parameters (thickness, lGI...)
by Daniel Klein 30 Sep '13

30 Sep '13

Dear FreeSurfer experts, thanks a lot for your solution. It works fine. I have some further questions to polynomial fitting with qdec, to prevent misunderstandings from my point of view. Only to be sure: 1) Linear effects of age: age as continuus factor. 2) Quadratic effects of age: age (quadratic) as continuus factor and age (linear) as nuisance factor. 3) Cubic effects of age: age (cubic) as continuus factor and age (linear) as nuisance factor. 4) Linear+quadratic+cubic effects together: i will have to use mri_glmfit with FSGD file. Best wishes Daniel...

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Re: [Freesurfer] Problem with downloading Xhemi programs
by Douglas N Greve 30 Sep '13

30 Sep '13

Hi Wen, are you using version 5.3? If so, then you will already have all the programs and atlases doug ps. Please remember to post to the list. thanks! On 09/29/2013 06:08 AM, wen.zhang55 wrote: > Dear Doug: > Sorry to bother you, but i have a trouble to download the programs > acoording to your instruction (Surface-based Interhemispheric > Registration:http://ftp.nmr.mgh.harvard.edu/fswiki/Xhemi) in > Freesurfer wiki. No relevant files in that FTP. So would you > please offer me another download link or kindly attach the program > files in the enclosure by email. Thank you very much! > All the best, > Wen Zhang > 2013-09-29 > ------------------------------------------------------------------------ > wen.zhang55 -- 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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Binary mask of the pons
by pfotiad＠nmr.mgh.harvard.edu 30 Sep '13

30 Sep '13

Hi FS Community, I was wondering whether there is a way to get a binary mask of the pons. Thanks in advance, Panos

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Freesurfer September 2013