Freesurfer November 2014

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

How is the actual thickness data stored?
by ye tian 17 Nov '14

17 Nov '14

Hello freesurfers, Suppose I do the following mris_preproc --fsgd gender_age.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.gender_age.thickness.10.mgh Then open the output file lh.gender_age.thickness.10.mgh in mathlab using result=MRIread('/path/rh.meditation.thickness.10.mgh'); Is it true that the actually thickness data is stored in result.volsize? Suppose that I have 27 subjects, is there a way to assign these numbers to their corresponding subjects? Thank you very much! Sincerely, Ye

2 1

temporal lobe exclusion
by O'Shea,Andrew 17 Nov '14

17 Nov '14

Hello all, I have heard about the issue of inaccuracy in the temporal lobes but never had problems myself until I recently tried processing a dataset from an outside group. On this data, the pial boundary are severely underestimated in the temporal lobes. It is worse right when the temporal lobes are coming into view as you slice back from the front of the brain along the coronal plane. I have attached a screenshot to show what I mean. Basically sections of the medial temporal lobe (greater than the hippocampus/amygdala area) and lateral temporal lobe are not included in the surfaces. The GM/WM contrast does not look very prominent in the t1 images. Is there any options we can specify which will lower the needed manual edits. I tried the ‘-mprage’ flag but that didn’t seem to help. Right now we have tried adding lots of control points but that doesn’t fix the issue 100%. Thanks for the help! -Andrew

2 1

prefrontal cortex label
by Anna Jonsson 17 Nov '14

17 Nov '14

Dear group, Is there a way to create a prefrontal cortex label in fresurfer? if so, please tell me the exact steps to do so, I am very confused. Thank you, Anna

3 5

Books
by Alex Spedding 17 Nov '14

17 Nov '14

Hi, Are there any books you could recommend that give an overview of some of the techniques Freesurfer uses? My research involves structural MRI so other books related to that would be good if you know any. I've got a couple of books on functional MRI analysis which I think are somewhat useful, as (I think) fMRI contain sMRI data though I could be completely wrong as I'm pretty new to this. Any book recommendations will be appreciated! Cheers, Alex

1 0

DICOM file selection for Recon-all
by Mattevada, Sravan 14 Nov '14

14 Nov '14

Hello Freesurfers, I am a beginner and have a question about the dicom file I need to select to do the recon-all process. I ran dcmunpack on the DICOM files I have with the following result Institution RADIOLOGY ASSOCIATES-CDI 1 LOCALIZER3PLANE 5 20 40 0.546875 ROW 180 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000000/IM000003 2 T1SESAG 8 345 90 0.8984375 ROW 140 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000001/IM000011 3 T2TSEAX 85 4170 180 0.8984375 ROW 110 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000002/IM000011 4 T1SEAX 8 410 90 0.8984375 ROW 140 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000003/IM000011 5 T2FLAIRAX 117 9000 180 0.8984375 ROW 130 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000004/IM000011 6 T2FL2DAXHEMO 27 855 20 0.8984375 ROW 80 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000005/IM000011 7 AXep2d_diff_2scan_trace 98 4100 90 1.796875\1.796875 COL 1260 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000006/IM000011 8 AXep2d_diff_2scan_trace_ADC 98 4100 90 1.796875\1.796875 COL 1260 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000007/IM000011 9 T2TSECOROBL 87 4260 180 0.4296875 ROW 110 /home/freesurfer/Desktop/9160/DICOM/PA000000/ST000000/SE000008/IM000011 I don't have one specific .dcm file to run the recon-all command The directory structure on the CD that I have has the 9 Folders (SE00000, SE000001 ...) Each folder has 6 - 25 files (IM00000, IM00000 ...) There are a total of 225 files When I use the software that came with the CD to see the images, I can see that each folder has series of images in different angles of the skull (different resolutions) Does recon-all use all the 225 images in all the folders? If yes how do I know which of the above dcmunpack results is the best option to start the recon-all process? I appreciate your help. Thanks Sravan Sravan Mattevada, MSCS Computer Prog. Analyst III UNT Health Ph . 817 735 0499

3 2

registration problem
by SHAHIN NASR 14 Nov '14

14 Nov '14

Hi, For one of my subjects, I have noticed a misalignment between sig.nii and orig.mgz when I try to show the sig map using either tkmedit (as below): cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Analysis tkmedit-sess -s ../Subjects/auil2 -a OriExp_TR3_1p5mm_PR -c ANG_90_45 or tkmedit-sess: cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Subjects tkmedit auil_anat orig.mgz -overlay auil2/bold/OriExp_TR3_1p5mm_PR/ANG_90_45/abs_sig.nii.gz -reg auil2/bold/register.dof6.dat~ I checked the registration file for this subjects and I don't see this problem there. tkregister2 --reg ../Subjects/auil2/bold/register.dof6.dat~ --mov ../Subjects/auil2/bold/template.nii.gz --surf I also checked the brain.mask and it covers the whole brain and looks fine to me. I also checked my other subjects and their results are fine. Do you have any idea why this is happening? P.S.: I process my data in in nmr-dev-env but I have also checked the above lines in nmr-stable53-env and problem is still there. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

Prefrontal white matter
by Alshikho, Mohamad J. 14 Nov '14

14 Nov '14

Hi Freesurfers, I want to calculate the FA in a VOI 8 mm3 in the left and right prefrontal white matter areas. My plan is to derive a mask for that area from aseg.mgz then I will register this mask to the FA map to calculate the FA value. Is it possible to derive like this mask from aseg.mgz and can I control the dimensions of that mask? thanks a lot Mohamad

3 7

Cortex/volume parcellation
by Octavian Lie 14 Nov '14

14 Nov '14

Dear all, Is there a way to generate random or seed-based whole cortical (surface) or brain (volumetric) parcellations in freesurfer or plugins, generating n equal area (volume) scouts, where the user can select the n? Thank you, Octavian

2 1

Freesurfer YouTube lecture slide download link 404
by Alex Spedding 14 Nov '14

14 Nov '14

Hi, Sorry if this is the wrong place to put this - never used a mailing list before - but I've been watching the FreeSurfer lectures on Youtube. The link to download the slides in the Introduction Lecture ( https://www.youtube.com/watch?v=GywOKtfKZIU ) the only one I've watched so far is broken. If you could fix the link that would be appreciated. Thank you, Alex Spedding

2 3

Data requirements
by will brown 13 Nov '14

13 Nov '14

Hi all, I have structural data that has a slice thickness of 5mm and spacing between slices of 5mm (there are around 30 dicom images). I ran it through recon-all but the output was bad. Is it possible to create surfaces from such data? Or is the bad output the answer to this question... Thanks, Will

2 1

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Freesurfer November 2014