Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

matlab dependencies
by Siddharth Srivastava 07 Dec '08

07 Dec '08

Hi all, 1) which steps of the freesurfer processing pipeline depend on/ use matlab for execution? I am trying to find out if we have to have matlab installed on all the computing nodes on our cluster here, or, if there is just one step, we can process it locally, and submit the downstream steps back to the cluster. 2) if anyone would like to share their experiences with running freesurfer on a cluster/grid computing environment, I would be happy to know, and maybe optimize my computing environment based on your recommendations 3) If there a canonical list of dependencies for the output generated by the -localGI flag. I was wondering if, if LGI is the only thing i need at the end, do i have to let freesurfer run through the entire processing steps? I mean, i do need other outputs as well, but can i chose a subset of processing steps based on what i would ultimately be using? :-) best regards, sid.

2 1

overlay
by luketseng＠gmail.com 07 Dec '08

07 Dec '08

hi, how do i overlay a .mgz image over an image in qdec so i can compare the two?

1 0

Two PhD positions in Neuroimaging of healthy aging and Alzheimer’s disease.
by Jose Luis Cantero Lorente 07 Dec '08

07 Dec '08

Dear Freesurfers, The Laboratory of Functional Neuroscience at the Department of Physiology, Anatomy and Cell Biology, University Pablo de Olavide, Seville (Spain), invites applications for two full-time PhD positions to work in neuroimaging (structural and functional) of healthy and pathological aging. Our interests are focused on the development of novel analysis procedures for the advanced analysis of cerebral white and grey matter anatomy and pathology, and the translation of these techniques in the study of healthy aging and Alzheimer's disease. Candidates will take a lead role in the analysis of structural and diffusion tensor MRI studies, as well as integrating this information with PET and cortical neurophysiology. This will be possible thanks to an ongoing longitudinal study that involves healthy elderly, mild cognitive impairment, and mild to moderate Alzheimer’s disease patients. Applicants should have a background in MRI-PET analysis techniques (Freesurfer, FSL, SPM, etc.), computer programming and statistical methods. Knowledge of Matlab is strongly preferred. Additional skills such as manual tracing methods of brain structures will be positively considered. Interest in clinical neuroscience and cognitive function would be also appreciated. Positions are funded for 2 years, available immediately, and have the option of extension. To apply please email a detailed CV to Dr. Jose L. Cantero, e-mail: jlcanlor(a)upo.es Two letters of recommendations will be required during the selection process. Best, Jose L. Cantero --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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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

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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

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