Freesurfer

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30132 discussions

co-registration: SWI images with FLAIR
by Ayaz, Muhammad 01 Oct '13

01 Oct '13

Dear All, Can I co-register SWI with FLAIR images using Freesurfer? thanks Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.

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Re: [Freesurfer] Transparency surface
by Arnaud Boré 01 Oct '13

01 Oct '13

Hi, Is there a way to see both side of the activation with a brain which looks like the pial ? Without inflated maybe I'm not really familiar with tksurfer. So far I used tksurfer fsaverage6 lh inflated by default. Thank you. Arnaud 2013/10/1 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Arnaud > > can you in general cc the list on these questions so that others can > answer. > > What you are trying to do is what the inflated surface is designed for. I > don't think the transparency thing would work - it would just be confusing > > > cheers > Bruce > > > On Tue, 1 Oct 2013, Arnaud Boré wrote: > > Hi Bruce, >> I added two pictures so you can see what I referred to. >> When I display the main surface, I'm able to see my activation. But when >> using the pial >> surface, it's hard to see the activation. I thought that if I could >> change the transparency of >> the surface, I will be able to see the other side (i.e., hidden in the >> sulci) of the >> activation (as shown in the main surface). >> >> Thank you for your answer. >> >> Arnaud >> >> >> >> 2013/10/1 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Arnaud >> >> why would transparency help? You should be able to view the overlay >> on any surface >> without transparency (the overlay defines the colors displayed on >> the surface). >> Can you explain further why the normal display in tksurfer doesn't >> do what you >> want? >> >> cheers >> >> Bruce >> >> On Tue, 1 Oct 2013, Arnaud Boré wrote: >> >> Dear Freesurfer experts, >> Using tksurfer I open an inflated surface and I display the >> pial >> surface. >> Then I load an overlay but I'm not able to see it correctly. >> Is it >> possible >> to put a transparency/opacity value for the surface so I can >> see >> better my >> overlay ? >> >> Thank you for your help >> >> Arnaud Bore >> >> >> >> >> >> 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<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. >> >> >> >> >> -- >> Arnaud BORE >> Research assistant >> Cellulaire : (001) 514-647-8649 >> >> >> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649

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Re: [Freesurfer] Question about preproc-sess -no-subcort-mask
by Leila Reddy 01 Oct '13

01 Oct '13

Hi Doug, I don't think that could have happened as I only found out about the no-subcort-mask option yesterday (after I had done all the original analysis). I have just re-run all the analyses for the same subject with the same commands on the two machines (output of bugr for the 2 machines is below). I had deleted everything from this subject's bold directory except the f.nii and para.para files for each run, so that everything is re-analyzed. I get the same problem as before. I attach a screen capture of freeview with my bold/analysis.mni/mask.nii overlaid on freesurfer/average/mni305.cor.mgz from the two machines. As you can see, they are different. They only look the same if I re-run the analysis on snowleopardv5.3.0 with preproc-sess -no-subcort-mask. Thanks again, Leila Machine 1: --------------------------------------------------------------------- FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Kernel info: Darwin 10.8.0 i386 --------------------------------------------------------------------- Machine 2: --------------------------------------------------------------------- FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.0.0 x86_64 --------------------------------------------------------------------- ________________________________ Date: Mon, 30 Sep 2013 17:48:15 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Question about preproc-sess -no-subcort-mask To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5249F19F.3070503(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed They do have the same default. Note that if you run preproc-sess with -no-subcort-mask and then run it again without -no-subcort-mask it will not generate a new file. Could that have happened? doug

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Freeview questions
by Jonathan Holt 01 Oct '13

01 Oct '13

Simply to make sure, 1) Is there no way that one can edit two volumes simultaneously similarly to tkmedits aux+main volume brush? 2) When editing voxels in freeview, is there anyway to have the cursor behave the same way it does in navigation mode. That is, I'd like to be able to see exactly where I'm editing in all 3 views, rather than just the one I'm editing in. Best, Jon

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Transparency surface
by Arnaud Boré 01 Oct '13

01 Oct '13

Dear Freesurfer experts, Using tksurfer I open an inflated surface and I display the pial surface. Then I load an overlay but I'm not able to see it correctly. Is it possible to put a transparency/opacity value for the surface so I can see better my overlay ? Thank you for your help Arnaud Bore

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missing eTIV in asegstats2table
by Daniel Ferreira 01 Oct '13

01 Oct '13

Hi, I just run my first asegstats2table in version 5.3 of FS. Is not eTIV included in the generated file anymore? I know that I can get eTIV with mri_segstats --subject subjid --etiv-only but, is it any way to get the values for all my subjects in a text file as asegstas2table does? Thanks a lot Dani

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(no subject)
by Valentina Ciullo 01 Oct '13

01 Oct '13

-- Dott.ssa Valentina Ciullo Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportamentale IRCCS Fondazione Santa Lucia via Ardeatina 306 - 00179 Roma Tel. +39(0)651501101 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com<http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

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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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