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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.

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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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mri_binarize VS mri_extract_label
by Palzes, Vanessa 28 Feb '12

28 Feb '12

Could someone please explain to me the difference between mri_binarize and mri_extract_label? I had been using mri_extract_label to create ROI masks of cerebral white matter (2 and 41). I recently became aware that this would give me a label with 0 and 128. I tried mri_binarize (with the same matchvals 2 and 41) and it gave me a label of 0 and 1. However, when comparing the two in tkmedit, it appears as though the mask I created using mri_binarize includes more of the corpus callosum region in mid-sagittal slices. I've tried this on a couple different subjects, so I do not think it is limited to one person. Is this a typical difference between the two commands? And if so, which one is recommended for extracting white matter masks? Also to note that before running either of these commands, I also convert the aseg.mgz to the subject's native space (using rawavg.mgz as a template). The commands I ran are the following: mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz mri_extract_label aseg-in-rawavg.mgz 2 41 cerebral_wm.nii mri_binarize --i aseg-in-rawavg.mgz --match 2 41 --wm --o cerebral_wm_binarize.nii On another note, I was wondering if there is a way to create a probability map for the white matter. That is, instead of getting a binary (0s and 1s) mask, I would get the probability of each voxel being part of the white matter ROI with values ranging from 0 to 1. Thanks for your help, Vanessa Palzes Staff Research Associate Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155

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qdec and Intracranial volume correction - error message
by Mahinda Yogarajah 28 Feb '12

28 Feb '12

Dear Experts, I am trying to carry out a simple 2 group (conrol and patient) analysis with ICV as nuisance factor, and thickness as the dependent variable. However whenever I include ICV (inputed by following the qdec tutorial and the generate stats table) I get the following output and error message: ------------------------------------------------------------------ lh-Avg-Intercept-thickness ----------------------- Does the average thickness differ from zero? 1.000 1.000 0.000 0.000; lh-Avg-thickness-IntraCranialVol-Cor ----------------------- Does the correlation between thickness and IntraCranialVol, accounting for diagnosis, differ from zero? 0.000 0.000 1.000 1.000; lh-Diff-Patients-Control-Intercept-thickness ----------------------- Does the average thickness differ between Patients and Control? 1.000 -1.000 0.000 0.000; lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol ----------------------- Does the thickness--IntraCranialVol correlation differ between Patients and Control? 0.000 0.000 1.000 -1.000; ninputs = 40 Checking inputs nframestot = 40 Allocing output Done allocing nframes = 40 Writing to /home/myogaraj/freesurfer/qdec/Untitled/y.mgh gdfReadHeader: reading /home/myogaraj/freesurfer/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 IntraCranialVol 1.42401e+06 259214 Class Means of each Continuous Variable 1 diagnosisPatients 1343236.0559 2 diagnosisControl 1497089.0952 INFO: gd2mtx_method is dods Reading source surface /home/myogaraj/freesurfer/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /home/myogaraj/freesurfer/qdec cmdline mri_glmfit --y /home/myogaraj/freesurfer/qdec/Untitled/y.mgh --fsgd /home/myogaraj/freesurfer/qdec/Untitled/qdec.fsgd dods --glmdir /home/myogaraj/freesurfer/qdec/Untitled --surf fsaverage lh --label /home/myogaraj/freesurfer/fsaverage/label/lh.aparc.label --C /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Avg-thickness-IntraCranialVol-Cor.mat --C /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Diff-Patients-Control-Intercept-thickness.mat --C /home/myogaraj/freesurfer/qdec/Untitled/contrasts/lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol.mat sysname Linux hostname localhost.localdomain machine x86_64 user myogaraj FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/myogaraj/freesurfer/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /home/myogaraj/freesurfer/qdec/Untitled/qdec.fsgd labelmask /home/myogaraj/freesurfer/fsaverage/label/lh.aparc.label maskinv 0 glmdir /home/myogaraj/freesurfer/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/myogaraj/freesurfer/qdec/Untitled Loading y from /home/myogaraj/freesurfer/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /home/myogaraj/freesurfer/qdec/Untitled/Xg.dat Normalized matrix condition is 175.031 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148025 voxels in mask Saving mask to /home/myogaraj/freesurfer/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 73649.347769 DOF = 36 Starting fit and test Fit completed in 0.0710833 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995672, ar1std=0.001628, gstd=6.144582, fwhm=14.469384 Writing results lh-Avg-Intercept-thickness maxvox sig=19.391 F=349.349 at index 102911 0 0 seed=1330322022 lh-Avg-thickness-IntraCranialVol-Cor maxvox sig=-3.43147 F=15.4402 at index 109705 0 0 seed=1330322022 lh-Diff-Patients-Control-Intercept-thickness maxvox sig=3.99329 F=19.0823 at index 28994 0 0 seed=1330322022 lh-Diff-Patients-Control-Cor-thickness-IntraCranialVol maxvox sig=-3.79353 F=17.7548 at index 129172 0 0 seed=1330322022 mri_glmfit done ninputs = 4 Checking inputs nframestot = 4 Allocing output Done allocing nframes = 4 Writing to /home/myogaraj/freesurfer/qdec/Untitled/contrasts.sig.mgh reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) gdfReadHeader: reading /home/myogaraj/freesurfer/qdec/Untitled/y.fsgd INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: NOT demeaning continuous variables Continuous Variable Means (all subjects) 0 IntraCranialVol 1.42401e+06 259213 Class Means of each Continuous Variable 1 diagnosisPatients 1343236.3158 2 diagnosisControl 1497089.0476 MatrixMultiply: m1 is null! No such file or directory --------------------------------------------------------- Can anyone advise ? Thanks. Mahinda

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Re: [Freesurfer] ?h.dpial.ribbon.mgz not found
by Douglas N Greve 28 Feb '12

28 Feb '12

It will do it's best, how well depends on the size of the resection. FS it assuming that the input is an intact (though perhaps diseased) brain. Away from the resection, it will probably do ok. Near the resection, it will probably fail, but you can probably fix it manually. doug octavian lie wrote: > > Thank you, Doug, > > One unrelated question: can I run freesurfer on postoperative T1 > MPRAGE sequences, where the relationship of the gray to white matter > (out-in) is disrupted at the site of resection? If so, can you share > any good advice on parameters to adjust? > Thank you, > > Octavian. > > > > > On Mon, Feb 27, 2012 at 10:14 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Octavian, recon-all does not use --save_distance by default. You > can have it add --save_distance to the mris_volmask command line > using the "expert options". Run recon-all with -help to get more info. > doug > > octavian lie wrote: > > Dear all, > to follow up on my prior message below, I must say that I > called the recon-all -autorecon-all command remotely through a > automatic matlab routine in which freesurfer is one leg, with > the command nohup. For some reason, when doing this, the step > mris_volmask was run without the option --save_distance hence > no ?h.dpial.ribbon.mgz fille was created. To fix this, I > manually entered the following command in the linux terminal: > mris_volmask--label_left_white 2 --label_left_ribbon 3 > --label_right_white 41 --label_right_ribbon 42 --save_ribbon > --save_distance SUB002, which created the output files needed. > Now, do you know why running recon-all -all remotely would > exclude the option --save_distance for mris_volmask. Is there > any way to fix this in the freesurfer itself, so that I do not > have to change the matlab code? > Thank you, also see my message below. > Octavian. > On Sat, Feb 25, 2012 at 6:46 PM, octavian lie > <octavian.lie(a)gmail.com <mailto:octavian.lie@gmail.com> > <mailto:octavian.lie@gmail.com > <mailto:octavian.lie@gmail.com>>> wrote: > > Dear Bruce & FreeSurfers, > I ran freesurfer (86x64_64 centos version 5.1.0) on my > new linux > box (Ubuntu 11.10 64 bit, NVIDIA GEforce GTX 580, no CUDA > for now) > using recon-all -all; it went on for 8 hours, I got the message > (Recon complete without errors) in the output.txt file in my > subject directory. However, when trying to use mri_convert or > tkmedit to see the lh.dpial.ribbon.mgz, there was an error > (could > not open file). I searched for the file in all the /mri > folder and > the whole file system on my box, could not find it. I found > lh.ribbon.mgz, rh.ribbon.mgz, and ribbon.mgz, but not the > dpial.ribbon.mgz file or any other ?.ribbon.mgz variety. > I appreciate your suggestions. > Octavian. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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

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question TRACULA
by j janssen 28 Feb '12

28 Feb '12

Hi, TRACULA gives pathstats.txt which includes *weighted* averages, mentioned on the wiki as: "weighted average over the entire support of the path distribution". question: weighted for what (is it the probability)? thanks, -joost

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