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30081 discussions

BrainSeg Volume Clarification
by Cook, Bernie 07 Jul '16

07 Jul '16

All, Upon looking at online forums and the FreeSurfer wiki, I have come to the understanding that "BrainSeg" volume in the aseg.stats file includes all cortical and subcortical gray matter, cerebellar gray matter; cortical, subcortical and cerebellar white matter and white matter hypointensities; and all ventricle volumes, but excludes the brain stem. When using the aseg.stats file for included subject "bert" to check my understanding of which volumes are used, I cannot seem to produce identical "BrainSegVol-to-TIV" ratios. I am adding the following volumes, all in mm^3, to obtain the brain volume: TotalGrayVol: 658087.056198 CorticalWhiteMatterVol: 485627.161537 Left-Lateral-Ventricle: 6562.6 Left-Inf-Lat-Vent: 228.3 Left-Cerebellum-White-Matter: 15708.2 3rd-Ventricle: 997.5 4th Ventricle: 1714.2 Right-Lateral-Ventricle: 6039.9 Right-Inf-Lat-Vent: 160.3 Right-Cerebellum-White-Matter: 15694.5 5th-Ventricle: 14.1 WM-hypointensities: 1002.6 Sum of individual measures: 1191836.418 Output of BrainSegVol: 1193318 And when normalizing the subject's brain volume by the eTIV measure (1594882.911364), I obtain the following: Individual measures: 0.7473 BrainSegVol-to-eTIV: 0.7482 Is there a reason that these two measurements are slightly off? I'm wondering whether there's certain volumes used for BrainSegVol that I missed, or ones that I included that would not be present in the output. Moreover, I'm wondering whether this could potentially be a result of using surface volumes (BrainSegVol) versus using both surface and voxel-space calculations (my addition method). Any help is appreciated. Thank you in advance. Best, [1455168447449_PastedImage] Bernard L. Cook Biomedical Engineering | Class of 2017 BMES at Ohio State | Professional Development Chair '16-'17 IBRC | Undergraduate Research Assistant 440-623-4710 cook.1327(a)osu.edu<mailto:cook.1327@osu.edu>

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continuity in volumes converted from labels
by MIKHAEL Shadia 07 Jul '16

07 Jul '16

Hello, I am interested in the cortical parcellations at the pial (grey matter) and white matter layers I have extracted grey matter (pial) and white matter (white) labels for a gyrus (right superior frontal gyrus, label 2028) mri_annotation2label --subject s1/12copy --hemi rh --labelbase ./12copy/label/rh.cortex --surface pial mri_annotation2label --subject s1/12copy --hemi rh --labelbase ./12copy/label/rh.cortex --surface white then converted the above 2 files (renamed to ...-wm and ...-gm) for the superior frontal gyrus to nifti's for viewing in other applications mri_label2vol --label ./label/rh.cortex-028.label --o rh-cortex-028-rsfg-wm.nii --identity --temp ./mri/T1.mgz mri_label2vol --label ./label/rh.cortex-028.label --o rh-cortex-028-rsfg-gm.nii --identity --temp ./mri/T1.mgz My goal is to run some statistics on 2 nifti's, which requires continuity in the nonzero voxels, in at least 1 of the 3 directions (x/y/z). This isn't the case for this gyri, particularly at the pial layer (shown in blue in the attachment). Is there a way in which this could be achieved? Have I missed any steps? Many thanks in advance. Shads The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Design Matrix Creation
by Timothy Hendrickson 07 Jul '16

07 Jul '16

Hi Doug, I just wanted to make sure that we were on the same page. I may have been a little unclear in what I would ideally like to do. For #2 what I would like to do is take into account age slopes and total intracranial slopes for gender, and age slopes and total intracranial slopes for diagnosis. I was not implying that I wanted diagnosis and gender to interact. Assuming that you understood this previously could you please explain why you would model the matrix this way? I do not fully understand. Respectfully, -Tim >I did not get the same matrix. Here's how I would do it >Columns 1-16 model the intercepts for all your classes >Columns 17-20 model the ages for your gender-x-diagnosis subclasses >Columns 21-24 model the ICV for your gender-x-diagnosis subclasses On 07/06/2016 02:04 PM, Timothy Hendrickson wrote: > Freesurfer Support, > > Thank you for your support with my previous line of questions regarding > design matrix creation. > I have manually created another design matrix and want to ensure that I > designed it correctly. > > An example of my FSGD file is as follows below: > Class SITE 1-Male-Control > Class SITE 1-Male-PATIENT > Class SITE 1-Female-Control > Class SITE 1-Female-PATIENT > Class SITE 2-Male-Control > Class SITE 2-Male-PATIENT > Class SITE 2-Female-Control > Class SITE 2-Female-PATIENT > Class SITE 3-Male-Control > Class SITE 3-Male-PATIENT > Class SITE 3-Female-Control > Class SITE 3-Female-PATIENT > Class SITE 4-Male-Control > Class SITE 4-Male-PATIENT > Class SITE 4-Female-Control > Class SITE 4-Female-PATIENT > Variables age_at_scan total_intracranial_volume > study site levels = 1, 2, 3, 4 > gender levels = Male, Female > diagnosis levels = PATIENT, Control > age_at_scan = covariate age > total_intracranial_volume = covariate total intracranial volume > > What I would ideally like to do is: > > 1) Take into account offset differences amongst diagnosis, gender, and study > site. > > 2) Allowing a difference in age slope, and total intracranial volume slope > amongst the diagnosis and gender levels. > > 3) Modeling the age slope and total intracranial volume slope as the same for > the study site levels. > Let's image that the first participant is from site 1, Male, and control, and > is 12 and has a TIV of 30,000. > The second participant is from site 2, Female, and PATIENT, and is 14, and > has a TIV of 25,000. > My understanding of the design matrix would be as follows: > 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 30000 0 0 0 > 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 25000 > -Tim > > >Yes, create your matrix manually. > > > >Those matrix lines are not quite right. The ages are in the correct > >column, but you need a 1 somewhere in columns 1-8 to indicate the class > >(ie, site/dx) that the subject is in. > On 05/26/2016 12:57 PM, Timothy Hendrickson wrote: > > Hi Doug, > > > > Thank you for such a prompt response. Just to be clear you are > > recommending that I manually create the matrix file right? > > > > If so I want to ensure that I am understanding how to design the > > matrix file properly. > > > > Let's imagine that the first participant is a control and is 13 and > > the second is a patient and is 15. My understanding is that the matrix > > file would be as follows: > > 0 0 0 0 0 0 0 0 13 0 > > 0 0 0 0 0 0 0 0 0 15. > > > > -Tim > > Previous correspondences are below: > > > > You'll need a regressor for each of the 8 classes you describe below. > > You can use mri_glmfit to generate this (Xg.dat file) > > You'll need two more regressors for age, one for each diagnosis. If a > > subject (ie, row) is a control then the two values will be AGE 0. If the > > subject of the row is a patient, then the two values will be 0 AGE. You > > can then set up a Controls-Patients age (ie, interaction between dx and > > age) contrast like > > [0 0 0 0 0 0 0 0 1 -1] > > On 05/24/2016 02:30 PM, Timothy Hendrickson wrote: > > > > > > Freesurfer Support, > > > > > > I'd like to create a design matrix for a group analysis outside of the > > > DODS and DOSS models. I understand that in order to do this the -X > > > flag must be used. However, I have been unable to find examples of how > > > to do this. > > > > > > I am hoping to reveal a difference in thickness or gyrification > > > amongst a clinical population. The data set contains two factors: > > > diagnosis, and study site and one covariate: age. Diagnosis has two > > > levels: controls, and patients. Study site has four levels, one level > > > for each location the data has been collected from. > > > > > > What I would ideally like to do is: > > > > > > 1) Take into account offset differences amongst diagnosis and study site. > > > > > > 2) Allowing a difference in age slope amongst the diagnosis levels > > > > > > 3) Modeling the age slope as the same for the study site levels > > > > > > My FSGD file is designed as follows > > > > > > Class SITE 1-Control > > > Class SITE 1-PATIENT > > > Class SITE 2-Control > > > Class SITE 2-PATIENT > > > Class SITE 3-Control > > > Class SITE 3-PATIENT > > > Class SITE 4-Control > > > Class SITE 4-PATIENT > > > Variables age_at_scan > > > > > > study site levels = 1,2,3 and 4 > > > diagnosis levels = PATIENT and Control > > > age_at_scan = covariate age > > > > > > Any advice would be greatly appreciated. > > > > > > Respectfully, > > > > > > Tim > > > > > > -- > > > Timothy Hendrickson > > > Department of Psychiatry > > > University of Minnesota > > > Mobile: 507-259-3434 <tel:507-259-3434> (texts okay) > >

2 1

mapping a surface from fsaverage_sym to the subject's native surface
by Ali-Reza Mohammadi-Nejad 07 Jul '16

07 Jul '16

Dear Freesurfer experts, Based on the FS wiki, I calculated the cortical thickness difference between the lh and rh of a subject.Now, I want to use the “mris_apply_reg” command to map the “left-right difference” from fsaverage_sym back to the subject's native surface.Unfortunately, I did not find the appropriate options of this command to do this work.Thanks for any help. Best regards,Ali-Reza Ali-Reza Mohammadi-Nejad Pre-doctoral research fellow Radiology and Neurology Research Henry Ford Health System Detroit, MI 48202, USA

3 3

make_average_template error
by Chatzi, Vasiliki 07 Jul '16

07 Jul '16

* Hello freesurfer developers, I am trying to compute the average_subject template described in the freesurfer wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject) I have located all the subjects' directories in one folder named All_data_baseline. Then I set SUBJECTS_DIR to this folder using the command setevn SUBJECTS_DIR ./ ,and then I defined the subjects using the command setenv SUBJECTS = (subject1 subject2 ...). Finally I run the command make_average_subject --out avgsubject. The directory avgsubject was created but then I received the following error: error.log: MRISread (.//subject1/surf/lh.sphere.reg): could not open file mris_make_template: could not read surface file .//subject1/surf/lh.sphere.reg error as it appears on the terminal: output subject: avgsubject mri_add_xform_to_header -c auto .//avgsubject/mri/mni305.cor.mgz .//avgsubject/mri/mni305.cor.mgz INFO: extension is mgz tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory #@# Making lh registration template --------- tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory /homedirectory/All_data_baseline/avgsubject tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory mris_make_template -norot -annot aparc lh sphere.reg subject1 tee: .//avgsubject/scripts/make_average_surface.log: No such file or directory not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization... processing subject subject1 (1 of 313) reading spherical surface .//subject1/surf/lh.sphere.reg... MRISread(.//subject1/surf/lh.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file .//subject1/surf/lh.sphere.reg No such file or directory ERROR: make_average_surface I did search the make_average_subject --help and the mail archive but I have not yet found a solution. Please accept my apologies if there is one but I have not noticed. I am using version freesurfer-5.3.0 in a Linux 7.1 with 48 core memory. I was wondering if you could possibly provide any advice for troubleshooting this error. Best wishes, Vasiliki

2 1

LGI Summary Statistics
by Timothy Hendrickson 07 Jul '16

07 Jul '16

Freesurfer Support, I have seen previous message threads on extracting LGI measurements across ROIs, however I have yet to find anything which would provide a summary LGI across an entire hemsphere. Other measurements like cortical thickness have a measurement like this. Is there a measurement like this for LGI? If I take the mean of all of the ROIs would that be equivalent to a hemispheric LGI measure? Thanks! -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

2 1

FOV Size Discrepancy
by Tamara Tavares 07 Jul '16

07 Jul '16

Hello! I was hoping someone can provide me with some clarification on an issue I have been having with the FOV size. I have a database of scans which I am running through recon-all cross-sectionally. The majority of the scans have an FOV of 256x256x208; however, when I run them through recon-all I get an error message indicating that the FOV is larger than 256 (282x282x228). When I use the -cw256 flag, recon-all runs through successfully. I do not understand why recon-all thinks the FOV is larger then it is. I double checked that the FOV size is 256 using the mri_info command line and the database information. Does anyone know why recon-all is listing a larger FOV size? Thank you in advance for your help. Tamara

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question about exporting volumes
by Dorsa Haji Ghaffari 07 Jul '16

07 Jul '16

Hi, I was able to segment the MRI successfully, now I am trying to isolate the thalamus and export it out of FS as a volume. Is there a way to do that in FS? Thank you Dorsa

3 4

Question about Thalamus segmentation
by Dorsa Haji Ghaffari 07 Jul '16

07 Jul '16

Hi, I am trying to segment the thalamus into its nuclei such as VLA , VLP and VIM. I see those labels available in the atlas but I do not get any of them in my segmentation. Does anyone have any idea how to do that? Thank you Dorsa

2 1

Error with local Gyrification Index (lGI)
by Mahtab Farahbakhsh 07 Jul '16

07 Jul '16

Dear FreeSurfer, I am trying to calculate LGI for my images, but it seems like that it doesn't work. I have tried everything, but it's still giving me the same error. I'm using FreeSurfer on a mac and my Matlab version is R2016a. When I try to run "recon-all -s <subj> -localGI", I get this error: ERROR: Matlab is required to run mris_compute_lgi!. I have done these so far: PATH=/Applications/MATLAB_R2016a.app/bin/matlab:$PATH export PATH And my $PATH is: /Applications/MATLAB_R2016a.app/bin/matlab:/usr/local/fsl/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/opt/X11/bin: No such file or directory And when I write getmatlab, I get this: ERROR: Cannot find matlab. Does not exist or is not in path. My original Matlab is in the /Applications folder and I also have a folder named "matlab" in my FreeSurfer folder. Would you please guide me what I should do? Best Regards, Mahtab.

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