Freesurfer

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30088 discussions

Repost: question regarding my contrast
by Jacobs H (NP) 07 Feb '12

07 Feb '12

Dear FreeSurfers, I have been doing some basic cortical thickness analyses, which all went good. Now I want to analyze some additional things, and I want to make sure that my contrast files are ok. Could you help me out or give me advice? So, I have three groups (control - MCI - Alzheimer) and I want to examine the effect of blood pressure on cortical thickness for each group separately (corrected for age centered). Thus, I would make three different fsgd files with this contrast:0 1 0 Then I want to compare how blood pressure affects the group differences in cortical thickness (controls vs MCI / MCI vs AD/ controls vs AD) when controlling for age: would that be: 0.5 -0.5 -0.5 0.5 0 0 ? Every help is greatly appreciated! Thank you Best 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 ================================================ _______________________________________________ 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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Large part of brain missing from wm.mgz and surfs
by Nicole Senecal 07 Feb '12

07 Feb '12

Hi all, My lab is just starting to use Freesurfer, and are finding that a lot of our recon-all jobs are needing a fair amount of editing. We've run into a problem that we can't figure out how to address - on several of our brains, a large chunk (up to 2/3 of the brain) is missing from the wm.mgz file and from surfs, although it IS present in the brainmask.mgz volume. Do we need to add control points manually to the entire brain? Why would this happen on multiple files? thanks, Nicole

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kvlQuantifyHippocampalSubfieldSegmentations.sh
by Rob Tennyson 07 Feb '12

07 Feb '12

Hi Experts, Is there a way to add the CA-4/DG subfield to the output generated by kvlQuantifyHippocampalSubfieldSegmentations.sh? Running the command for an individual subject outputs this subfield, but I wanted to make sure there wasn't an easier route before I start manually entering each subject's data into a text file. Thanks! Rob -- Rob Tennyson Research Coordinator, Bar Lab Massachusetts General Hospital Phone: 617-724-0413

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Problem viewing hippo-subfields
by Rob Tennyson 07 Feb '12

07 Feb '12

Hi Experts, So I found a similar question posted in December, but I was not able to fix my own results based on the reply to that message. Anyway, I ran "recon-all -s -bert -hippo-subfields" (with my filename) and finished without error. Now, I am attempting to view the segmentation in freeview using: cd $SUBJECTS_DIR/bert/mri freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt ew using: But I get the error messages: "Failed to load posterior_left_*" and "Failed to load posterior_right_*" The folder (bert/mri) has all of the correct segmentation files. Is there something I am doing wrong or some way to troubleshoot this problem? Thanks! Rob -- Rob Tennyson Research Coordinator, Bar Lab Massachusetts General Hospital Phone: 617-724-0413

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Hippo-subfield fault
by Rob Tennyson 07 Feb '12

07 Feb '12

Hi All, Sorry for the novice question, but I began running the hippo subfield on some data that had already been run through recon-all yesterday and have run into some problems. It is confusing because they function completed one of my subjects but has not successfully completed any others that I have tried. At various points I receive the following: "Done transforming mesh Rasterizing Levenberg-Marquardt... /usr/local/freesurfer/stable5_1_0/bin/kvlSegmentHippocampalSubfields.sh: line 18: 2941 Segmentation fault kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt failed to do kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt Linux shimshon 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:10:13 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux" *(shimshon is the linux box I am running the script on)* * * Let me know if more info is needed, I am not sure if this is a common error or not. I saw a similar question was asked in November but could not find a solution for it. Thanks for any help! Rob -- Rob Tennyson Research Coordinator, Bar Lab Massachusetts General Hospital Phone: 617-724-0413

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Registration for Upcoming Freesurfer Course, April 2-4
by Allison Player 07 Feb '12

07 Feb '12

The Freesurfer group will be offering a three-day Freesurfer Tutorial and Workshop, April 2-4 at the Martinos Center in Charlestown, MA. A description of the course, the tentative schedule, and the link to the registration website can be found here: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription There are 6 spots remaining and registration is on a first-come, first-serve basis. If you are not one of these 6, you will be put on a waiting list and will be notified if a spot becomes available (which happens fairly often). Payment is due immediately upon registration. Payment arrangements are to be made with Stacey Ladieu (sladieu(a)nmr.mgh.harvard.edu) but please cc me on your emails with her so I can update your payment status accordingly. General questions about the course or registration can be sent to me. If we have not heard from you by February 13th, we will give your spot to the next person on the waiting list. Announcements about course openings are made to the Course mailing list first. If you would like to sign up for that list, you can do so here: http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi Regards, The FreeSurfer Team

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A question about testing the installation
by Nooshin Zadeh 07 Feb '12

07 Feb '12

Hi all, I have a question about FS installation. Finally I installed FS, but not sure it is complete. For testing FS installation, when I wrote tkmedit bert orig.mgz, It says: Couldn't create output file .xdebug_tkmeditReading /Applications/freesurfer/tktools/tkm_common.tcl Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/tktools/tkUtils.tcl Also I can not close the tksurfer window. Can you please give me advices? Thanks Here is what it brings for tksurfer tksurfer bert rh pial Couldn't create output file .xdebug_tksurfersubject is bert hemi is rh surface is pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Applications/freesurfer surfer: can't create file surfer.log in cwd surfer: surfer.log created in /tmp surfer: session root data dir ($session) reset to: surfer: /tmp checking for nofix files in 'pial' Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=132934, faces=265864 surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /Applications/freesurfer/tktools/tksurfer.tcl Reading /Applications/freesurfer/tktools/tkm_common.tcl Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % surfer: Error sending tcl command MoveToolWindow 646 674: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 609 682: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 581 686: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 552 689: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 520 689: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 489 690: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 457 690: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 428 691: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 404 694: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 394 696: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 394 697: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 394 698: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 393 698: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 393 699: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 392 699: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 391 700: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 390 701: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 389 701: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 389 702: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 388 702: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 388 703: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 386 704: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 389 704: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 398 702: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 423 698: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 456 697: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 497 697: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 543 697: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 600 697: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 664 697: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 727 697: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 787 697: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 852 697: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 906 697: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 949 697: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 991 697: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1032 697: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1069 692: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1101 687: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1130 682: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1154 677: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1172 674: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1185 673: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1195 673: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1202 673: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1206 673: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1208 673: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1209 673: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1210 673: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1211 673: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1212 673: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1215 673: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1223 671: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1234 670: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1247 668: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1264 665: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1280 662: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1295 659: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1309 657: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1319 657: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1325 657: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1329 657: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 1330 657: can't invoke "wm" command: application has been destroyed -- Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * *

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Re: [Freesurfer] What does trac-all do on the file 'bvecs'?
by Xiangzhen Kong 07 Feb '12

07 Feb '12

Could you give me something about the transpsition here? I checked the code flip4fsl and found there are two kinds of sign. line 59. set sign = `echo $inorient | sed "s/[LAS]/+\ /g; s/[RPI]/-\ /g"` line 99. set sign = `echo $inorient | sed "s/[RAS]/+\ /g; s/[LPI]/-\ /g"` e.g. When the orientation of DWI is LPS, we have to transform data to RAS. ($fslplipx=1) The first sign = +-+ and the second sign = --+. So I have to multiple the bvecs(extracted from DICOM) by [-1 -1 +1], but NOT [+1 -1 +1]. Why are they different? Thanks! 2012-02-04 Xiangzhen Kong 发件人： Anastasia Yendiki 发送时间： 2012-02-04 00:48:58 收件人： Xiangzhen Kong 抄送： freesurfer 主题： Re: [Freesurfer] What does trac-all do on the file 'bvecs'? When the DWIs are transformed to LAS and processed with eddy_correct, the same transformations are applied to the respective bvecs. On Fri, 3 Feb 2012, Xiangzhen Kong wrote: > Hi, all~ > ? > I use trac-all with .nii data, not dicom. So I have to specify the bvecs and > bvals in the config file. > Trac-all requires a bvecs file in 3 columes, but FSL need that in 3 raws. > I wonder what does trac-all do on the bvecs file that I specify. > And I have check the code 'trac-preproc' and the log, but found nothing, > except copy and Eddy-current "correction". > ? > ps: The orientation of my dicom and .nii fils are both LPS, and the bvecs is > read from the DICOM header via nibabel. > But FSL requires LAS. I thinks trac-all have done the transposition on the > bvecs somewhere. > What orientation of bvecs does trac-all need when run with .nii files? > ? > Thanks! > ? > Xiangzhen > ? > 2012-02-03 > ? > > 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] Conversion of an mgh file to nii (fwd)
by Bruce Fischl 07 Feb '12

07 Feb '12

FYI ---------- Forwarded message ---------- Date: Tue, 7 Feb 2012 09:15:37 -0500 From: Ziad Saad <saadz(a)mail.nih.gov> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Conversion of an mgh file to nii I just realized my post got rejected from the message list since I I am not a subscriber. Could you throw it up there for me? thanks z On Feb 7, 2012, at 9:10 AM, Bruce Fischl wrote: > thanks Ziad > Bruce > On Tue, 7 Feb 2012, Ziad Saad wrote: > >> Greetings, >> >> I am not sure what is causing the problem but if you are trying to create a volume where you have a non zero value at some coordinate you can use: 3dUndump with options -xyz and -master . This will create a mask volume with a non-zero value at specified xyz locations, or around these locations depending on the options you use. The -xyz option is used to specify the coordinate which you get from your seed location in FreeSurfer and the master option specifies the dataset grid that your output should match - the time series for regression analysis. >> This assumes, that the X Y Z of the dipole location corresponds to the same anatomical location as the X Y Z in your volumes. Note that AFNI uses RAI for axis orientation, so you'll likely need to negate the 1st two dimensions of the X Y Z you have at hand. >> You could also create volumetric masks with more complicated routes, such as 3dSurf2Vol but I don't see the reason for that. >> >> cheers, >> Ziad >> >> On Feb 6, 2012, at 7:16 PM, Bruce Fischl wrote: >> >>> you could do the same if you sampled your test.nii into the volume. At >>> the moment it's a surface overlay, so as Doug points out no volume loader >>> will know what to do with it. You need the surface geometry/topology to >>> properly display it. If you want to sample it into the volume I think you >>> want mri_surf2vol. >>> >>> cheers >>> Bruce >>> >>> On Mon, 6 Feb 2012, Omer Tal wrote: >>> >>>> Hey Bruce, >>>> >>>> Maybe I can give more background information to help explain what I am >>>> trying to do here. >>>> >>>> I have a subject which I have both MEG and fMRI data on. When I >>>> reconstructed my subject, I chose a dipole as a seed location and used it >>>> for my MEG analysis. Now I want to use the same location as a seed for my >>>> fMRI analysis, so I created an mgh file which had the value of 1 only in >>>> the FS vertex/dipole corresponding to my seed. I can view all versions of >>>> it, mgh, mgz and nii w/ no problem on tksurfer. On FSL though, I can't. >>>> >>>> The reason I went this approach is when I wanted to use the same >>>> aparc_aseg parcellations in my fMRI data, all i had to do is use >>>> mri_convert on the aprac+aseg.mgz and I had a nice nii file I could view >>>> in FSL or AFNI overlaying my fMRI data and use the same ROIs in both >>>> modalities for analysis. Therefore, I thought it would make sense to do >>>> the same here, and create a mgh/mgz file and convert to an nii to get my >>>> mask that I could use in AFNI. >>>> >>>> Do you believe my approach is impractical? >>>> >>>> For loading in AFNI, all I did was afni test.nii. >>>> >>>> Thank you, >>>> Omer >>>> >>>>> Ziad: any idea why Omer can open this file in tksurfer but not afni? Omer: >>>>> I don't think you'll be able to load it in FSL since it's essentially a >>>>> surface. Can you give us details about how you are trying to load it in >>>>> AFNI? Are you using SUMA? >>>>> >>>>> On Mon, >>>>> 6 Feb 2012, Omer Tal wrote: >>>>> >>>>>> Sorry, that was the wrong error description (for the AFNI portion). >>>>>> >>>>>> It just says cannot open dataset test.nii >>>>>> >>>>>> Well, if it doesn't work on FSL or AFNI, I would guess it is the >>>>>> conversion process from FreeSurfer. I don't think anyone on AFNI knows >>>>>> mri_convert or mri_sruf2surf. >>>>>> >>>>>> Honestly just trying to get support for your product for a very simple >>>>>> task, not sure where else I could find someone who would know how to use >>>>>> FS outputs. >>>>>> >>>>>> Omer >>>>>> >>>>>> >>>>>>> It sounds like it is doing the right thing. The geometry is going to be >>>>>>> bogus because it is a surface. You should post to the AFNI list. >>>>>>> doug >>>>>>> >>>>>>> Omer Tal wrote: >>>>>>>> Hey Bruce, >>>>>>>> >>>>>>>> So the mgh file loads fine in tksurfer (shows proper map) for the >>>>>>>> given >>>>>>>> subject, and so does its corresponding mgz (created from mri_convert). >>>>>>>> >>>>>>>> In FSL there is no physical error, but when loading in the nii file, >>>>>>>> the >>>>>>>> X >>>>>>>> location is in ~786XX instead of the typical -128 to 128 or something >>>>>>>> close, Y has no slices to go through at all, and Z seems for the most >>>>>>>> part >>>>>>>> normal (240 slices centered at 0). >>>>>>>> >>>>>>>> When I was trying to load those in AFNI, it simply said "ncols 157373 >>>>>>>> in >>>>>>>> volumes exceeds 32768" even though the reshape has been done. >>>>>>>> >>>>>>>> Thank you, >>>>>>>> Omer Tal >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> does it load ok in freesurfer (in tksurfer)? What error do you get in >>>>>>>>> AFNI/FSL? If it >>>>>>>>> >>>>>>>>> On Mon, 6 Feb 2012, Omer Tal wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>>> Hey Doug, >>>>>>>>>> >>>>>>>>>> Here is what I type it the terminal and what pops back at me. The >>>>>>>>>> error >>>>>>>>>> shows up later when trying to load (either though AFNI or FSL). >>>>>>>>>> >>>>>>>>>> mri_surf2surf --sval test.mgh --tval test.nii --reshape-factor 241 >>>>>>>>>> --s >>>>>>>>>> 111123 --hemi lh >>>>>>>>>> >>>>>>>>>> srcsubject = 111123 >>>>>>>>>> srcval = test.mgh >>>>>>>>>> srctype = >>>>>>>>>> trgsubject = 111123 >>>>>>>>>> trgval = test.nii >>>>>>>>>> trgtype = >>>>>>>>>> srcsurfreg = sphere.reg >>>>>>>>>> trgsurfreg = sphere.reg >>>>>>>>>> srchemi = lh >>>>>>>>>> trghemi = lh >>>>>>>>>> frame = 0 >>>>>>>>>> fwhm-in = 0 >>>>>>>>>> fwhm-out = 0 >>>>>>>>>> label-src = (null) >>>>>>>>>> label-trg = (null) >>>>>>>>>> OKToRevFaceOrder = 1 >>>>>>>>>> Reading source surface reg >>>>>>>>>> /home/otal/raweegmeg/structuralDB//111123/surf/lh.sphere.reg >>>>>>>>>> Loading source data >>>>>>>>>> INFO: trgsubject = srcsubject >>>>>>>>>> Saving target data >>>>>>>>>> Reshaping 241 (nvertices = 157373) >>>>>>>>>> Saving to test.nii >>>>>>>>>> >>>>>>>>>> Thank you, >>>>>>>>>> Omer Tal >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> what's your command line and terminal output? >>>>>>>>>>> >>>>>>>>>>> Omer Tal wrote: >>>>>>>>>>> >>>>>>>>>>>> Tried both, but neither gave a proper nii image. >>>>>>>>>>>> >>>>>>>>>>>> Any other ideas? >>>>>>>>>>>> >>>>>>>>>>>> Omer Tal >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>> That particular number factors to 241 and 653, so use one of >>>>>>>>>>>>> those >>>>>>>>>>>>> as >>>>>>>>>>>>> the reshape factor to surf2surf. >>>>>>>>>>>>> doug >>>>>>>>>>>>> >>>>>>>>>>>>> Omer Tal wrote: >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> Hey Doug, >>>>>>>>>>>>>> >>>>>>>>>>>>>> I believe for this patient/hemisphere the number of vertices is >>>>>>>>>>>>>> 157373. >>>>>>>>>>>>>> >>>>>>>>>>>>>> What is the workaround in the case my number of vertices is >>>>>>>>>>>>>> unluckily >>>>>>>>>>>>>> a >>>>>>>>>>>>>> prime? >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>> Omer Tal >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Omar, how many vertices? The reshape only works if the >>>>>>>>>>>>>>> number >>>>>>>>>>>>>>> is >>>>>>>>>>>>>>> not >>>>>>>>>>>>>>> prime (actually the largest prime factor has to be less than >>>>>>>>>>>>>>> 2^15. >>>>>>>>>>>>>>> doug >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Omer Tal wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hey Bruce, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thank you for the prompt response. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The line is as follows: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> mri_convert -it mgh -ot nii test.mgh test.nii. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Since I do agree that the issue is arising from the NIFTI bit >>>>>>>>>>>>>>>> limit, >>>>>>>>>>>>>>>> i >>>>>>>>>>>>>>>> tried doug's suggestion of >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> mri_surf2surf --sval test.mgh --tval test.nii --reshape-factor >>>>>>>>>>>>>>>> 6 >>>>>>>>>>>>>>>> --s >>>>>>>>>>>>>>>> subject_name --hemi lh >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> But it doesn't seem to solve the problem. even though now i >>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>> load >>>>>>>>>>>>>>>> it >>>>>>>>>>>>>>>> through FSL without it failing and quitting, the image is >>>>>>>>>>>>>>>> faulty >>>>>>>>>>>>>>>> w/ >>>>>>>>>>>>>>>> over >>>>>>>>>>>>>>>> 78,000 data points in the X direction, none in Y, and 240 in >>>>>>>>>>>>>>>> Z. >>>>>>>>>>>>>>>> At >>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>> point, Doug told him to send the file in and no more follow-up >>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>> shown... >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Please advise. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thank you very much, >>>>>>>>>>>>>>>> Omer Tal >>>>>>>>>>>>>>>> UCSD Keck Center for Functional MRI >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Omer >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> what file are you trying to convert? What is your entire >>>>>>>>>>>>>>>>> command >>>>>>>>>>>>>>>>> line >>>>>>>>>>>>>>>>> with output and what problems do you have? Nifti >>>>>>>>>>>>>>>>> unfortunately >>>>>>>>>>>>>>>>> only >>>>>>>>>>>>>>>>> allows >>>>>>>>>>>>>>>>> 16 bits for the width/height/depth/nframes, so surface >>>>>>>>>>>>>>>>> overlays >>>>>>>>>>>>>>>>> can't >>>>>>>>>>>>>>>>> usually fit as nvertices x 1 x 1 x nframes since nvertices > >>>>>>>>>>>>>>>>> 2^16 >>>>>>>>>>>>>>>>> (or >>>>>>>>>>>>>>>>> 2^15 >>>>>>>>>>>>>>>>> signed). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> cheers >>>>>>>>>>>>>>>>> Bruce >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Mon, 6 Feb 2012, Omer >>>>>>>>>>>>>>>>> Tal wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hey there, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I am trying to convert an mgh file I created into an nii >>>>>>>>>>>>>>>>>> volume >>>>>>>>>>>>>>>>>> so >>>>>>>>>>>>>>>>>> I >>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>> load it in AFNI. I was trying to use mri_convert, which I >>>>>>>>>>>>>>>>>> have >>>>>>>>>>>>>>>>>> used >>>>>>>>>>>>>>>>>> previously to make nii volumes from my aparc+aseg and it >>>>>>>>>>>>>>>>>> worked >>>>>>>>>>>>>>>>>> great, >>>>>>>>>>>>>>>>>> but >>>>>>>>>>>>>>>>>> this time the resulting file is faulty. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I've noticed a previous thread where someone ran into a >>>>>>>>>>>>>>>>>> similar >>>>>>>>>>>>>>>>>> problem, >>>>>>>>>>>>>>>>>> and it had to do w/ too many vertices existing for NIFTI, >>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>> Doug >>>>>>>>>>>>>>>>>> suggested using mri_surf2surf, but it didn't work for that >>>>>>>>>>>>>>>>>> guy >>>>>>>>>>>>>>>>>> or >>>>>>>>>>>>>>>>>> me >>>>>>>>>>>>>>>>>> (at >>>>>>>>>>>>>>>>>> which point I think he was sending you files). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Seems like it should be something common and trivial, but I >>>>>>>>>>>>>>>>>> can't >>>>>>>>>>>>>>>>>> get >>>>>>>>>>>>>>>>>> it >>>>>>>>>>>>>>>>>> too work, any suggestions? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>> Omer Tal >>>>>>>>>>>>>>>>>> UCSD Keck Center for Functional MRI >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> 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 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> 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 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> 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 >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> 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 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> 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 >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>> >>>> >>>> >> >> >> >>

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problem defining mrs voxel using mri_volsynth
by Todd Jolly 07 Feb '12

07 Feb '12

Hi all, Recently I have been trying to reconstruct a mrs voxel using mri_volsynth using the VOIpositions given in the .rda file. The VOI co-ordinates are as follows: VOIPositionSag 31.6911 VOIPositionCor -25.1448 VOIPositionTra 24.5879 When I input these co-ordinates into mri_volsynth the voxel is in the wrong location. However when I reverse the sign for the Sag and Cor positions then the voxel is very close to right position. After a lot of trial and error I found that after inverting the sign for the X and Y co-ordinates, I have to then +1 on all 3 positions in order for the synthesised volume to be in the correct position. So using the three positions shown above I have to use the following command: mri_volsynth --dim 18 18 18 1 --pdf const --c_ras -30.6911 26.1448 25.5879 --o filename Can anyone explain why I have to reverse the sign and add 1 in order for the voxel to be in the correct location? Is it something to do with using the dcm2nii converter? Also is it normal for the .rda to give the co-ordinates for the centre of the voxel rather than the top corner of the voxel? Thanks Todd

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