Freesurfer May 2013

freesurfer@nmr.mgh.harvard.edu

174 participants
299 discussions

T or Z values in QDEC
by Kelly, Philip 17 May '13

17 May '13

Dear Freesurfer list members, Within QDEC I have found a number of clusters that show significantly different cortical thickness and local gyrification between two groups. The cluster summary exhibits the p value, coordinates and other information regarding the cluster, however I wanted to report the t or z values and was unsure in finding or computing this from QDEC. The p-value must be computed from one of these scores but I could not find it to be reported in any of the output. Searching on the mailing list and tutorials, I could not find an easy solution to this. Thanks for your time and I look forward to hearing back. All the best, Philip Kelly

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incomplete forceps
by Roschinski, Benjamin 17 May '13

17 May '13

Dear Freesurfer experts, we have a problem with the forceps. After the first trac-all we had a forcpes minor with a really unusually structure so we tried to fix it with an rerun of the trac-all. The result was a forceps minor with a third thigh in the sagittal axis. We did a second rerun and now the forceps minor normalized. Our problem is that we don´t know if we should do more trac-all reruns by other patients with difficult tracula or how we should interpret this result. Do you have any ideas to solve this? The second problem is that we have many many tracula results with incomplete forcepes minor or major. We know that the forcepes are the most difficult tracts because of the curvature but do you have some ideas to fix that problem? Kind regards Benjamin

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recon-all error: Correcting Defect 2
by Sudhin A. Shah 17 May '13

17 May '13

Hi, I got the following error: CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Thanks, S

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conversion from ascii to surface
by Tina Jeon 17 May '13

17 May '13

Dear Doug, Nick, and all, I am trying to convert a surface from Amira to freesurfer in order to visualize a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and need to convert those into surfaces that can be read by tksurfer. Do you have any suggestions for how I could do the conversion? Thank you in advance! All the best Tina Jeon PhD Candidate UT Southwestern Medical Center '14 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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T or Z values in QDEC
by Kelly, Philip 17 May '13

17 May '13

1 0

Freesurfer hemisphere surface flipping
by Hamza Alshuft 16 May '13

16 May '13

Dear Freesurfers and experts Does anyone know how to flip hemisphere surfaces (cortical thickness) for with-in group analysis? I am analysing a cohort of unilateral chronic knee OA patients and want to within-group correlate the cortical thickness changes with the mechanical pain threshold. (A perfect study would be having only Rt. or Lt. knee pain and then the hypothesis would be a contra-lateral brain cortical thickness changes) but since I have a mixed patients of Rt and Lt knee pain, I want to flip only one group to match the other and make them all as they were having same laterality, and then do a correlation analysis using QDEC! Any help will be much appreciated Thanks Hamza This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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F Problem running : mri_cc -aseg.auto_
by Ray, Siddharth 16 May '13

16 May '13

Hi, I am new to freesurfer and was trying to run it on couple of my subjects but I am stuck (for last 40 hrs) at stage "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/sray2/Desktop/combirx/cr052_ip_output/mri/transforms/cc_up.lta cr052_ip_output" it seems. The last few lines of the log file were: searching scale 1 Z rot 9.9 searching scale 1 Z rot 10.1 global minimum found at slice 122.0, rotations (-3.99, 3.36) final transformation (x=122.0, yr=-3.992, zr=3.355): 0.996 -0.059 -0.069 25.704; 0.058 0.998 -0.004 -3.212; 0.070 0.000 0.998 -51.078; 0.000 0.000 0.000 1.000; Have anyone came across this error before ? and know how to fix this. Please let me know. Thanks in advance. ~Siddharth Ray P.S. I have attached the log file here.

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5.3 mri_convert bug?
by Chris Steward 16 May '13

16 May '13

Hi, Tried running recon-all on two different linux systems and same error occurs in the mri_nu_correct.mni.log when running mri_convert on the nu1.mnc ie.. . . . Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 64 CV of field change: 0.000946853 Outputting Volume: ............................................................ mri_convert ./tmp.mri_nu_correct.mni.24934/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.24934/nu1.mnc orig_nu.mgz --like orig.mgz --conform ncopen: filename "./tmp.mri_nu_correct.mni.24934/nu1.mnc": Not a netCDF file miopen: MINC package entry point Error opening ./tmp.mri_nu_correct.mni.24934/nu1.mnc mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.24934/nu1.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.24934/nu1.mnc... Any help appreciated. Thanks, Chris

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Differences between FLIRT & bbregister-TRACULA outputs out of expected range
by Ali Ezzati 16 May '13

16 May '13

Hello FreeSurfers and TRACULA expert, I would be grateful if anyone could help me with my problem: I was able to run all the steps of TRACULA on several subjects without any error message. My problem is that the average FA/MD/RD/AD outputs are not in the same range as previous studies. For example, the average FA values for all the tracts are between 0.6 and 0.8, which I think is too high - especially since my population are elderly adults. I wonder if anyone else had the same issue and if anyone can help me what might be the source of the problem. While I was trying to narrow down the possible sources of error, I reran a couple of subjects registering with both "FLIRT" & "bbregister". I think in the latest version of tutorial "bbregister" is the preferred method. The results show very large differences between the 2 methods! Is this expected &/ normal? Although these are different from each other, both of them still are out of range (i.e. average FA value 20% more than literature), so registration method -alone- is not the source of my 1st problem. Thank you so much, Ali

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Fsaverage b0
by Fotiadis, Panagiotis 16 May '13

16 May '13

Hi FreeSurfer experts, I was wondering whether there is an average b0 scan in the fsaverage space or in the MNI space? Thank you, Panagiotis.

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Freesurfer May 2013