Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

ERROR! FOV=348.000 > 256
by Ray, Siddharth 18 Jun '13

18 Jun '13

Hi all, I am coming across this error for couple of my subjects: WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (240.00 mm, 240.00 mm, 347.20 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 348 slices. If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) ==================================================++++++++++++++++++++++++=============== $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/sray2/Data/50183/50183/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (0.468746, 0.468746, 1.4) mm size and (512, 512, 248) voxels. Data is conformed to 1 mm size and 348 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/sray2/Data/50183/50183/mri/orig.mgz... **************************************** ERROR! FOV=348.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux localhost.localdomain 2.6.32-71.el6.x86_64 #1 SMP Wed Sep 1 01:33:01 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 50183 exited with ERRORS at Sat Jun 15 06:02:30 CDT 2013 Do anyone know whats wrong and how can I fix this? Thanks in advance. -Siddharth

3 10

stuck on step to create surface
by Jane Qu 18 Jun '13

18 Jun '13

Hi freesurfers! I am new to freesurfer and have encountered a problem with surface generation. I am working with a non-human primate anatomical volume. I finished segmenting the white matter and am on this next step. I think, however, that the step where the surface is generated from wm.mgz is crashing (I started the process last night and it has not finished and does not appear to be moving forward). Does anybody know why this might be happening? How long should I expect this step to take? I have attached below some of the messages I'm receiving. Thanks in advance! Jane

3 2

Mapping annotation files from one subject to another
by Peter Savadjiev 18 Jun '13

18 Jun '13

Hello, I have an annotation file for fsaverage, which I would like to map it to a particular subject. What would be the best way to do so? I tried a combination of calls to mris_ca_train and mris_ca_label, but the latter gave me an error. First I ran mris_ca_train lh lh.sphere.reg fsaverage/label/<file>.annot fsaverage /tmp/<output>.gcs (where <file> and <output> are some file names) and that executed without any problems. Then I ran mris_ca_label <subject_id> lh lh.sphere.reg /tmp/<output>.gcs ./lh.<newfile>.annot (here <subject_id> is some subjects' name, and <output> and <newfile> are some names) and I got the error: could not open translation file $FREESURFER_HOME/Simple_surface_labels2002.txt Maybe there is a simpler way to perform this task? Or maybe an easy way to fix this error? Any help will be much appreciated. Thank you, Peter

3 5

ct.anat.nii file
by Borzello, Mia 18 Jun '13

18 Jun '13

Hi Freesurfers, I'm wondering if there is a way to figure out if a ct.anat.nii file is corrupt or not. I'm using MRICro as a viewer, and the file doesn't look right. Thanks, Mia

1 0

medial wall crossing surface
by celine＠nmr.mgh.harvard.edu 18 Jun '13

18 Jun '13

Hi Freesurfer team I am wondering if there would be a way to improve surfaces on the medial wall, not for the measurement of cortical thickness, but also for laminar analysis in the cortex. We would need them to be accurate even for the medial wall. What would you suggest? Thanks Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

2 5

Temporal Lobe Problem
by LIOR ZWANZIGER 18 Jun '13

18 Jun '13

Hi, I have scans of around 60 participants and about 75% percent of these have significant portions of their temporal lobe excluded. I have attached different slices from four different subjects to give you an idea of the typical scan I've been encountering, [though there are problems in minimally 10 slices for each participant and some exclusions can be found in more than 50 slices.] We are using FreeSurfer version 5.1.0. What is your advice, since there are so many slices for a large number of participants that would need to be edited? Extension of the watershed parameters, adding control points, or something else I haven't considered? I am hesitant to add control points for such a great number of participants. Thank you! Lior Zwanziger

2 1

Group Analysis
by Nooshin Zadeh 18 Jun '13

18 Jun '13

Dear Freesurfer group I am interested to do group analysis on my data. If I want to do inter-individual group analysis, what is the minimum number of subjects I need to have? Also if I want to do intra-individual analysis, what is the best way in FS? I appreciate your time and your help. Thanks a lot, Nooshin

1 0

recon-all error: mri_watershed (picture include)
by Sudhin A. Shah 18 Jun '13

18 Jun '13

Hi, This is the error I get: ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=96, z=161, r=9988 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 42408 RIGHT_CER CSF_MIN=1, CSF_intensity=17, CSF_MAX=27 , nb = 1512 LEFT_CER CSF_MIN=0, CSF_intensity=6, CSF_MAX=20 , nb = 2142 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=3, CSF_MAX=29 , nb = 17010 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 15750 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 5994 mri_watershed Error: GLOBAL region of the brain empty ! Please find attached a screenshot of the MRI Please advice, S

4 4

Re: [Freesurfer] Tracula bbr errors
by Douglas Greve 18 Jun '13

18 Jun '13

Hi Matt, was I supposed to get back to you on this? I generally leave these types of questions to Nick and Zeke. doug ps. Please post to the list instead of us indivudally. thanks! On 6/16/13 12:46 PM, Matthew Hoptman wrote: > Hi Dr. Greve, > Any news on the libboost_program_options.so.5 issue? I've encountered > it using mris_resample (as part of mri_cvs_register) using Linux Mint 14 > Best, > Matt

1 0

problem downloading Xhemi files
by amirhossein manzouri 18 Jun '13

18 Jun '13

Dear Doug, I can not download the files needed for Xhemi in mentioned link. Would you please advise how to download them? -- Best regards, Amir

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