Freesurfer

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30132 discussions

Re: [Freesurfer] hippocampus volume normalization question
by Douglas N Greve 29 Feb '12

29 Feb '12

You'll have to run it on each subject. Easy to do with a script. You can then cat the data into one fine (they are just text files). doug Rashmi Singh wrote: > Thanks Doug, > Do I need to run the following for each subject or can is there a way to > run it with input for all my subjects in one go to get the brain volume of > all my subject in one output file. > Thanks, > > > > On 2/29/12 10:15 AM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > > >> oh, sorry, I do remember now that we took that out (I think we put it >> back in for the next release). The work-around is to run >> >> mri_binarize --i brain.mgz --min 0.00001 --count count.dat --o junk.mgh >> >> You can delete junk.mgh. The file count.dat will have info about the >> number of voxels in the brain. It will have 4 numbers: >> #voxels in brain, brain volume (mm3), total # voxels in volume, and >> brain volume as a percent of total volume in the 3d a field of view. >> >> doug >> >> >> Rashmi Singh wrote: >> >>> Hello doug, >>> In the asegstats. Txt ( that got as in the table format with >>> information >>> on all subjects grouped together in a single .Xls file) I found >>> information on Total Gray vol but I don't see whole Brain volume. >>> Can you please suggest me where to get the whole brain volume. >>> Thanks, >>> Rashmi. >>> >>> >>> On 2/28/12 3:22 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: >>> >>> >>> >>>> In the aseg.stats file there is a value for the whole brain volume. >>>> doug >>>> >>>> Rashmi Singh wrote: >>>> >>>> >>>>> I would like know how can I get the sub-cortical volumes normalized >>>>> it >>>>> to >>>>> the whole brain. >>>>> Thanks, >>>>> Rashmi. >>>>> >>>>> On 2/28/12 3:14 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>> wrote: >>>>> >>>>> >>>>> >>>>> >>>>>> No, it does not. All volumes are volumes in native anatomical space. >>>>>> doug >>>>>> >>>>>> Rashmi Singh wrote: >>>>>> >>>>>> >>>>>> >>>>>>> Hello. >>>>>>> I am using FreeSurfer to generate subcortical volumes and cortical >>>>>>> thickness for my subjects. >>>>>>> Does FreeSurfer normalizes the subcortical volumes to the whole >>>>>>> brain >>>>>>> volume for each subjects. >>>>>>> Let me know. >>>>>>> For among subjects comparison I am assuming that the sub cortical >>>>>>> volumes generated for each subject are normalized to its own whole >>>>>>> brain volume. >>>>>>> >>>>>>> Thank you, >>>>>>> Rashmi. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> --------------------------------------------------------------------- >>>>>>> -- >>>>>>> - >>>>>>> >>>>>>> This document may contain information covered under the Privacy >>>>>>> Act, 5 >>>>>>> USC 552(a), and/or the Health Insurance Portability and >>>>>>> Accountability >>>>>>> Act (PL 104-191) and its various implementing regulations and must >>>>>>> be >>>>>>> protected in accordance with those provisions. Healthcare >>>>>>> information >>>>>>> is personal and sensitive and must be treated accordingly. If this >>>>>>> correspondence contains healthcare information it is being provided >>>>>>> to >>>>>>> you after appropriate authorization from the patient or under >>>>>>> circumstances that don't require patient authorization. You, the >>>>>>> recipient, are obligated to maintain it in a safe, secure and >>>>>>> confidential manner. Redisclosure without additional patient consent >>>>>>> or as permitted by law is prohibited. Unauthorized redisclosure or >>>>>>> failure to maintain confidentiality subjects you to application of >>>>>>> appropriate sanction. If you have received this correspondence in >>>>>>> error, please notify the sender at once and destroy any copies you >>>>>>> have made. >>>>>>> >>>>>>> >>>>>>> --------------------------------------------------------------------- >>>>>>> -- >>>>>>> - >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> >>>>>> >>>>>> >>>>>> 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. >>>>>> >>>>>> >>>>>> >>>>>> >>>>> ________________________________ >>>>> >>>>> This document may contain information covered under the Privacy Act, 5 >>>>> USC 552(a), and/or the Health Insurance Portability and Accountability >>>>> Act (PL 104-191) and its various implementing regulations and must be >>>>> protected in accordance with those provisions. Healthcare information >>>>> is >>>>> personal and sensitive and must be treated accordingly. If this >>>>> correspondence contains healthcare information it is being provided to >>>>> you after appropriate authorization from the patient or under >>>>> circumstances that don't require patient authorization. You, the >>>>> recipient, are obligated to maintain it in a safe, secure and >>>>> confidential manner. Redisclosure without additional patient consent >>>>> or >>>>> as permitted by law is prohibited. Unauthorized redisclosure or >>>>> failure >>>>> to maintain confidentiality subjects you to application of appropriate >>>>> sanction. If you have received this correspondence in error, please >>>>> notify the sender at once and destroy any copies you have made. >>>>> >>>>> >>>>> >>>>> >>>>> >>>> -- >>>> 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 >>>> >>>> >>>> >>>> >>> ________________________________ >>> >>> This document may contain information covered under the Privacy Act, 5 >>> USC 552(a), and/or the Health Insurance Portability and Accountability >>> Act (PL 104-191) and its various implementing regulations and must be >>> protected in accordance with those provisions. Healthcare information is >>> personal and sensitive and must be treated accordingly. If this >>> correspondence contains healthcare information it is being provided to >>> you after appropriate authorization from the patient or under >>> circumstances that don't require patient authorization. You, the >>> recipient, are obligated to maintain it in a safe, secure and >>> confidential manner. Redisclosure without additional patient consent or >>> as permitted by law is prohibited. Unauthorized redisclosure or failure >>> to maintain confidentiality subjects you to application of appropriate >>> sanction. If you have received this correspondence in error, please >>> notify the sender at once and destroy any copies you have made. >>> >>> >>> >>> >> -- >> 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 >> >> >> > > > ________________________________ > > This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. > > > -- 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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problem generate stats data tables
by Charlotte Bernard 29 Feb '12

29 Feb '12

Dear freesurfer users, I have tried to run "generate stats data tables", but I have that error message: asegstats2table --common-segs --meas volume --tablefile /home/charlotte/TROISCITES/DATA/FREESURFER/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 10049 10053 10079 10104 10105 10123 10130 10132 10138 10139 10168 10348 10824 10874 10902 10958 11457 11651 11889 12181 SUBJECTS_DIR : /home/charlotte/TROISCITES/DATA/FREESURFER Parsing the .stats files ERROR: The stats file /home/charlotte/TROISCITES/DATA/FREESURFER/10049/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files All the files "aseg" are present in my subjects directories. Can somebody help me? Thanks for all, Charlotte

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Re: [Freesurfer] hippocampus volume normalization question
by Douglas N Greve 29 Feb '12

29 Feb '12

oh, sorry, I do remember now that we took that out (I think we put it back in for the next release). The work-around is to run mri_binarize --i brain.mgz --min 0.00001 --count count.dat --o junk.mgh You can delete junk.mgh. The file count.dat will have info about the number of voxels in the brain. It will have 4 numbers: #voxels in brain, brain volume (mm3), total # voxels in volume, and brain volume as a percent of total volume in the 3d a field of view. doug Rashmi Singh wrote: > Hello doug, > In the asegstats. Txt ( that got as in the table format with information > on all subjects grouped together in a single .Xls file) I found > information on Total Gray vol but I don't see whole Brain volume. > Can you please suggest me where to get the whole brain volume. > Thanks, > Rashmi. > > > On 2/28/12 3:22 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > > >> In the aseg.stats file there is a value for the whole brain volume. >> doug >> >> Rashmi Singh wrote: >> >>> I would like know how can I get the sub-cortical volumes normalized it >>> to >>> the whole brain. >>> Thanks, >>> Rashmi. >>> >>> On 2/28/12 3:14 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: >>> >>> >>> >>>> No, it does not. All volumes are volumes in native anatomical space. >>>> doug >>>> >>>> Rashmi Singh wrote: >>>> >>>> >>>>> Hello. >>>>> I am using FreeSurfer to generate subcortical volumes and cortical >>>>> thickness for my subjects. >>>>> Does FreeSurfer normalizes the subcortical volumes to the whole brain >>>>> volume for each subjects. >>>>> Let me know. >>>>> For among subjects comparison I am assuming that the sub cortical >>>>> volumes generated for each subject are normalized to its own whole >>>>> brain volume. >>>>> >>>>> Thank you, >>>>> Rashmi. >>>>> >>>>> >>>>> >>>>> >>>>> ----------------------------------------------------------------------- >>>>> - >>>>> >>>>> This document may contain information covered under the Privacy Act, 5 >>>>> USC 552(a), and/or the Health Insurance Portability and Accountability >>>>> Act (PL 104-191) and its various implementing regulations and must be >>>>> protected in accordance with those provisions. Healthcare information >>>>> is personal and sensitive and must be treated accordingly. If this >>>>> correspondence contains healthcare information it is being provided to >>>>> you after appropriate authorization from the patient or under >>>>> circumstances that don't require patient authorization. You, the >>>>> recipient, are obligated to maintain it in a safe, secure and >>>>> confidential manner. Redisclosure without additional patient consent >>>>> or as permitted by law is prohibited. Unauthorized redisclosure or >>>>> failure to maintain confidentiality subjects you to application of >>>>> appropriate sanction. If you have received this correspondence in >>>>> error, please notify the sender at once and destroy any copies you >>>>> have made. >>>>> >>>>> ----------------------------------------------------------------------- >>>>> - >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> >>>> 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. >>>> >>>> >>>> >>> ________________________________ >>> >>> This document may contain information covered under the Privacy Act, 5 >>> USC 552(a), and/or the Health Insurance Portability and Accountability >>> Act (PL 104-191) and its various implementing regulations and must be >>> protected in accordance with those provisions. Healthcare information is >>> personal and sensitive and must be treated accordingly. If this >>> correspondence contains healthcare information it is being provided to >>> you after appropriate authorization from the patient or under >>> circumstances that don't require patient authorization. You, the >>> recipient, are obligated to maintain it in a safe, secure and >>> confidential manner. Redisclosure without additional patient consent or >>> as permitted by law is prohibited. Unauthorized redisclosure or failure >>> to maintain confidentiality subjects you to application of appropriate >>> sanction. If you have received this correspondence in error, please >>> notify the sender at once and destroy any copies you have made. >>> >>> >>> >>> >> -- >> 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 >> >> >> > > > ________________________________ > > This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. > > > -- 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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Re: [Freesurfer] mri_vol2surf issue
by Douglas N Greve 28 Feb '12

28 Feb '12

the way you have it set up, it is sampling on the gray/white boundary ("white" surface). You can sample midway into the ribbon with --projfrac 0.5 doug Omer Tal wrote: > Hey Doug, > > Attached is a picture showing the resulting surface file. Note that the > red regions correspond to the number 2 (white matter) and the yellow > regions correspond to numbers between 1000 and 1035 (gray matter). If the > conversion would be completed correctly, only numbers between the 1000 and > 1035 should come up on the surface. > > Thank you for your time and help, > Omer Tal > > > >> can you post a picture? >> >> Omer Tal wrote: >> >>> Hey Doug, >>> >>> Tried, no change unfortunately. >>> >>> >>> Here is the output, just in the case: >>> mri_vol2surf --src aparc+aseg.nii --surf orig --ref orig.mgz --regheader >>> 111123 --hemi lh --o test.mgh >>> srcvol = aparc+aseg.nii >>> srcreg unspecified >>> srcregold = 0 >>> srcwarp unspecified >>> surf = orig >>> hemi = lh >>> reshape = 0 >>> interp = nearest >>> float2int = round >>> GetProjMax = 0 >>> INFO: float2int code = 0 >>> INFO: changing type to float >>> Done loading volume >>> Computing registration from header. >>> Using /home/otal/raweegmeg/structuralDB//111123/mri/orig.mgz as target >>> reference. >>> Reading surface /home/otal/raweegmeg/structuralDB//111123/surf/lh.orig >>> Done reading source surface >>> Mapping Source Volume onto Source Subject Surface >>> 1 0 0 0 >>> using old >>> Done mapping volume to surface >>> Number of source voxels hit = 100537 >>> Writing to test.mgh >>> Dim: 157373 1 1 >>> >>> Thank you, >>> Omer Tal >>> >>> >>> >>> >>>> Hi Omer, >>>> Try removing "--srcreg identity" >>>> doug >>>> >>>> Omer Tal wrote: >>>> >>>> >>>>> Hey Doug, >>>>> >>>>> Test.nii is a volume nii (1x1x1mm) with values of interest per voxel, >>>>> created using the header from brain_T1.nii which was simply created by >>>>> using mri_convert from the subject's original brain.mgz. The *.nii >>>>> file >>>>> loads fine and matches the subject as expected. It is when trying to >>>>> go >>>>> back to surface, that things seem to get messy. >>>>> >>>>> Thank you very much for your time, >>>>> Omer Tal >>>>> Keck Center for Functional MRI, UCSD >>>>> >>>>> >>>>> >>>>> >>>>>> What is test.nii? How was it derived? >>>>>> >>>>>> Omer Tal wrote: >>>>>> >>>>>> >>>>>> >>>>>>> Hey all, >>>>>>> >>>>>>> I am running into a bit of a problem converting back from a volume >>>>>>> into >>>>>>> a >>>>>>> surface and was hoping someone would have some insight. >>>>>>> >>>>>>> I have an .nii volume for a given subject, and I want to convert it >>>>>>> into >>>>>>> a >>>>>>> surface mgh file, so i can view it on tksurfer. Since its the same >>>>>>> exact >>>>>>> subject, I figured it should be relatively easy, but in the >>>>>>> resulting >>>>>>> surface all the white matter and gray matter voxels are mixed >>>>>>> together >>>>>>> (looks like tiger pattern on tksurfer) in the entire brain. I would >>>>>>> point >>>>>>> out though that the gray matter voxels do show up in the correct >>>>>>> location >>>>>>> (i.e. a motor gray voxel in my volume still ends up in the motor >>>>>>> cortex >>>>>>> in >>>>>>> the mgh file), its just that they are surrounded with vertices which >>>>>>> have >>>>>>> white matter values. >>>>>>> >>>>>>> Any advice? >>>>>>> >>>>>>> Code: mri_vol2surf --src test nii --srcreg identity --ref T1.mgz >>>>>>> --regheader test_subj --hemi lh --o test.mgh >>>>>>> >>>>>>> Thank you very much for your help, >>>>>>> Omer Tal >>>>>>> Keck Center for Functional MRI, UCSD >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> >>>>>> >>>>>> >>>>>> 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: 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 >> >> >> > > > -- 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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Re: [Freesurfer] hippocampus volume normalization question
by Douglas N Greve 28 Feb '12

28 Feb '12

In the aseg.stats file there is a value for the whole brain volume. doug Rashmi Singh wrote: > I would like know how can I get the sub-cortical volumes normalized it to > the whole brain. > Thanks, > Rashmi. > > On 2/28/12 3:14 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > > >> No, it does not. All volumes are volumes in native anatomical space. >> doug >> >> Rashmi Singh wrote: >> >>> Hello. >>> I am using FreeSurfer to generate subcortical volumes and cortical >>> thickness for my subjects. >>> Does FreeSurfer normalizes the subcortical volumes to the whole brain >>> volume for each subjects. >>> Let me know. >>> For among subjects comparison I am assuming that the sub cortical >>> volumes generated for each subject are normalized to its own whole >>> brain volume. >>> >>> Thank you, >>> Rashmi. >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> This document may contain information covered under the Privacy Act, 5 >>> USC 552(a), and/or the Health Insurance Portability and Accountability >>> Act (PL 104-191) and its various implementing regulations and must be >>> protected in accordance with those provisions. Healthcare information >>> is personal and sensitive and must be treated accordingly. If this >>> correspondence contains healthcare information it is being provided to >>> you after appropriate authorization from the patient or under >>> circumstances that don't require patient authorization. You, the >>> recipient, are obligated to maintain it in a safe, secure and >>> confidential manner. Redisclosure without additional patient consent >>> or as permitted by law is prohibited. Unauthorized redisclosure or >>> failure to maintain confidentiality subjects you to application of >>> appropriate sanction. If you have received this correspondence in >>> error, please notify the sender at once and destroy any copies you >>> have made. >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> 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 >> >> >> >> 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. >> >> > > > ________________________________ > > This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. > > > -- 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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hippocampus volume normalization question
by Rashmi Singh 28 Feb '12

28 Feb '12

Hello. I am using FreeSurfer to generate subcortical volumes and cortical thickness for my subjects. Does FreeSurfer normalizes the subcortical volumes to the whole brain volume for each subjects. Let me know. For among subjects comparison I am assuming that the sub cortical volumes generated for each subject are normalized to its own whole brain volume. Thank you, Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

2 1

mri_vol2surf issue
by Omer Tal 28 Feb '12

28 Feb '12

Hey all, I am running into a bit of a problem converting back from a volume into a surface and was hoping someone would have some insight. I have an .nii volume for a given subject, and I want to convert it into a surface mgh file, so i can view it on tksurfer. Since its the same exact subject, I figured it should be relatively easy, but in the resulting surface all the white matter and gray matter voxels are mixed together (looks like tiger pattern on tksurfer) in the entire brain. I would point out though that the gray matter voxels do show up in the correct location (i.e. a motor gray voxel in my volume still ends up in the motor cortex in the mgh file), its just that they are surrounded with vertices which have white matter values. Any advice? Code: mri_vol2surf --src test nii --srcreg identity --ref T1.mgz --regheader test_subj --hemi lh --o test.mgh Thank you very much for your help, Omer Tal Keck Center for Functional MRI, UCSD

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Reposted question
by Antonella Kis 28 Feb '12

28 Feb '12

Hi Doug, Sorry to bother again and I hope I'm not becoming too annoying with my questions. I will be very grateful if you can advise what to do for the following: 1) I am still struggling to find a way to localize my clusters in other words to get the nearest cortical label(annotation) if I know the MNI coordinates on the MNI space. As a reminder I was trying to get a the nearest cortical label(annotation) on the CVS space since this data was registered on the CVS space but can I get their location on the MNI space if I have their coordinates without doing another registration to MNI? Can I use fsaverage or what should I do? 2) Can you please advise me what is the best way in catching the uncorrected clusters results from the sig.mgh for a structural study: Should I use the: mri_glmfit-sim \ --glmdir lh.GroupAnalysis_Thickness_15.glmdir \ --cache 2 pos \ --cwpvalthresh .99 \ --overwrite But in this case I am not getting all the clusters regarding their significance after correction by multiple comparison? I don't want the clusters from multiple comparisons just the uncorrected one. 3) For a paper to be published what is the recommended threshold (what people use in general) for the voxel-wise threshold of the clusters when running the perm or grf. Is a threshold of 3 acceptable (P<0.001) or in general I should use 2 (p<0.01)? Many thanks. AK

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Problem with conversion to mgz
by Hemant Bokil 28 Feb '12

28 Feb '12

I am trying to convert some dicom slices to mgz but am getting errors. From the errors it appears that mri_convert is looking for some metadata and that this metadata is corrupted. The MRs themselves look fine when I view them in Matlab. The full screen dump is below: mri_convert -it dicom -ot mgz DICOM_MR_DATA/MR2/MR20000.DICOM MR2 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from DICOM_MR_DATA/MR2/MR20000.DICOM... Starting DICOMRead2() dcmfile = DICOM_MR_DATA/MR2/MR20000.DICOM dcmdir = DICOM_MR_DATA/MR2 Ref Series No = 3 Found 83 files, checking for dicoms Found 80 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: -nan -nan -nan Second Sorting Counting frames nframes = 80 nslices = 1 ndcmfiles = 80 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=40.00, TE=8.00, TI=0.00, flip angle=40.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (nan, nan, -nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is -nan, matrix is: -1.094 -0.000 nan nan; -0.000 -1.094 nan nan; 0.000 0.000 -nan -nan; 0.000 0.000 0.000 1.000;

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mri_glmfit-sim and subject-override
by Tyler Manning 28 Feb '12

28 Feb '12

Hi, I am comparing asymmetries in fmri activation, and have been following your instructions as per https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019869.h… , but when it comes to the multiple correction with mri_glmfit-sim I get an error that the --subject-override command was not found. The version currently installed on the machine is 1.36.2.1 from 2011/03/28 and I can't find a download for the newer version mentioned in the email above. Has one been uploaded? Many thanks, Tyler Manning

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