Freesurfer

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30081 discussions

RE: for cortical thickness
by Zhang, Xiaochu (NIH/NIDA) [F] 05 Dec '08

05 Dec '08

Hi, FreeSurfer export, Thank you very much for response! Now, under some export's help, I used to the mri_surf2vol to transfer cortex thickness into nifti. The below line is what I used. mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon --template orig.mgz --volregidentity ${subid} --outvol lh.ribbon.nii I checked the result and found the voxel outside the gray matter is always zero and in the gray matter is about 0-3. Could you please do me a favor and tell me whether these data is cortex thickness or not? If they are cortex thickness, why are they always different. In my mind, it should be same in one direction because we calculate the distance between the white matter line and the gray matter line. Thanks a lot! All the best, Xiaochu

2 10

a display problem, again!
by Zhang, Xiaochu (NIH/NIDA) [F] 05 Dec '08

05 Dec '08

Because there is no response, I sent it again. I just checked the problem and guessed there is something wrong in the default setup. Is it corrected? what information do you want? Xiaochu Zhang PhD Visiting Research Fellow Neuroimaging Research Branch National Institute on Drug Abuse - IRP Biomedical Research Center 251 Bayview Blvd. Suite 200 (NIDA) Baltimore MD 21224 Tel: 443-740-2619 ________________________________ From: Zhang, Xiaochu (NIH/NIDA) [F] Sent: Thursday, December 04, 2008 6:44 PM To: Freesurfer Mailing List Subject: [Freesurfer] a display problem Hi Freesurfer expert, I just started to use freesurfer. I tried to follow the instruction to learn how to use "tksurfer". However, when I type "tksurfer bert lh inflated". Only a very small part of brain was showed (see the attachement). I do not know the reason. Could you please do me a favor and give me some hints? Thanks a lot! Xiaochu Zhang PhD Visiting Research Fellow Neuroimaging Research Branch National Institute on Drug Abuse - IRP Biomedical Research Center 251 Bayview Blvd. Suite 200 (NIDA) Baltimore MD 21224 Tel: 443-740-2619 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 2

Error in lh.thickness - rh.thickness not shown in qdec
by Julia Altenburg 05 Dec '08

05 Dec '08

Hi, when running qdec the following error shows up. It is possible to run the analysis for the lh. thickness and area but not for the same in rh. In the single subject folders the averages for rh. are missing. qcache did run without any error messages. I thought it could have something to do with the fsaverage or qcache, but changes within those didn't change the message. With -emacx I found out that there were problems within the lh. process allready. It seems to be the same error then the following I found something simmilar in the mailing list: ERROR: number of vertices in /usr/local/freesurfer/subjects/4964-14_recon/surf/lh.thickness does not match surface (138139,137319)ERROR: reading curvature file why is it that rh. isn't readable then? Is there anything then running the whole recon-all process again I could do? Thanks a lot in advance I'm thankful for any advice Julia

3 2

Question about recon-all
by Devdutta W 05 Dec '08

05 Dec '08

Hello, I am a new freesurfer user. I have been trying to run recon-all on our data and have been unable to do so because recon-all crashes everytime at the same spot. Here is the error I get when I run recon-all with autorecon1 or when I run it with -nuintensitycor *Iteration 1 Fri Dec 5 12:03:19 CST 2008 nu_correct -clobber ./tmp.mri_nu_correct.mni.8746/nu0.mnc ./tmp.mri_nu_correct.mni.8746/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8746/0/ nu_correct: couldn't find program "nu_estimate_np_and_em" nu_correct: couldn't find program "nu_evaluate" add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 486 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 489 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 521 add_default_args: warning: adding default arguments for unregistered program "nu_estimate_np_and_em" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 530 add_default_args: warning: adding default arguments for unregistered program "nu_evaluate" at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 530 spawn: error: program "nu_estimate_np_and_em" not registered at /usr/local/imsw/freesurfer/mni/bin/nu_correct line 60 ERROR: nu_correct Linux chinook 2.6.18-53.1.21.el5 #1 SMP Wed May 7 08:42:13 EDT 2008 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Fri Dec 5 12:03:19 CST 2008* I have made sure that the "nu_estimate_np_and_em" as well as "nu_evalutate" are both in the appropriate directory. I have also set the environment properly. Can anybody help me solve this? I appreciate any help or suggestions. Thank you, Dev

3 5

stable3
by jake＠nmr.mgh.harvard.edu 05 Dec '08

05 Dec '08

Hello! I was just wondering if there is anything going on with the stable3 environment, or any changes currently being tweaked. The reason is that I have a script for analysis that sometimes says "ispl failed" which usually resolves itself if I wait a day or two, but hasnt resolved as of yet. Thanks, Jake

2 1

a display problem
by Zhang, Xiaochu (NIH/NIDA) [F] 04 Dec '08

04 Dec '08

Hi Freesurfer expert, I just started to use freesurfer. I tried to follow the instruction to learn how to use "tksurfer". However, when I type "tksurfer bert lh inflated". Only a very small part of brain was showed (see the attachement). I do not know the reason. Could you please do me a favor and give me some hints? Thanks a lot! Xiaochu Zhang PhD Visiting Research Fellow Neuroimaging Research Branch National Institute on Drug Abuse - IRP Biomedical Research Center 251 Bayview Blvd. Suite 200 (NIDA) Baltimore MD 21224 Tel: 443-740-2619

1 0

mri_ca_normalize infinite loop
by Mishkin Derakhshan 04 Dec '08

04 Dec '08

Hi, I have one subject which seems to cause mri_ca_normalize to hang. I've checked and the registration to tal is okay, as is the brainmask. The subject in question does have large ventricles and lots of atrophy, which is what I'm assuming is causing the problem. Here are the last couple lines: finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (132, 66, 29) --> (194, 169, 199) and then it will just hang there with no errors or further screen output. I let it run for almost 24 hours (others took only 7) and I've tried on a couple different machines with no luck. any ideas on how to debug? thanks, mishkin freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0

2 1

quick follow-up
by Jared Price 04 Dec '08

04 Dec '08

Will missing header info affect the rebuild_gca_atlas script? I noticed it didn't like it if echo time, repetition time etc. didn't match. Also, I assume there is no difference, or minimal enough difference to ignore, in the 001.mgz file when converted from say nifti or straight from dicom. Correct?

2 1

missing information in volume headers
by Jared Price 04 Dec '08

04 Dec '08

Dear freesurfer gurus, I noticed something unusual in some of our data today. When the command mri_info was run on some of the orig.mgz volumes the values listed for echo time and flip angle in some of the scans were 0.00, even though there was a listing for repetition time. What could have caused this? Could misinformation in the header cause variation in the freesurfer processing of that scan? Cheers, Jared

3 2

vertex wise correction for multiple comparisons using permutation
by Lúcia Garrido 04 Dec '08

04 Dec '08

Dear Freesurfers, I'd like to correct for multiple comparisons vertex-wise instead of cluster-wise. Is it possible to do this using permutation (and not FDR)? I've seen in an e-mail from last year that the values of maximum statistic stored in the CSD file could be used for this purpose, and I'd be very grateful if you could let me know how. Many thanks, Lucia

2 1

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