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30132 discussions

MCSRCH ERROR
by Irwin, William 08 Aug '11

08 Aug '11

Hi- I'm at a bit of a loss as to how to address and/or fix these errors. The native input images are very good quality; the conversion to T1.mgz is fine; the brainmask.mgz is good, a bit of dura remained at the parietal/occipital region (very common); otherwise, the skull stripping is very clean. The recon-all "finished" but with errors as expected. Processing "continued" to the end, but there is no output except in /mri and /touch. Doing: #@# Skull Stripping First under "Computing MAP estimate using 3481 samples..." IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10327.2 tol 0.000010 Then several of the same under "EM alignment process ..." IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 3 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 4 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 5 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 017: -log(p) = 1145822.4 tol 0.000000 Then again at "Computing MAP estimate using 2772 samples..." IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 7006.0 tol 0.000010 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 838978.4 tol 0.000000 Thanks, Wil ____________________________________ William Irwin | Brain Imaging Coordinator UCSF | Memory and Aging Center 350 Parnassus Avenue, Suite 905 San Francisco CA 94143-1207 wirwin(a)memory.ucsf.edu | memory.ucsf.edu p: 415.476.1680 | f: 415.476.1816

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Defining the Calcarine and distances from it in the Hinds et al. V1 label
by Krish Singh 08 Aug '11

08 Aug '11

Dear All, I've been trying out the automatic V1 labelling using the Hinds et al. (NeuroImage, 2008 vol. 39 (4) pp. 1585-99) and, as far as I can tell it seems to work pretty well on our anatomical scans (In general I'd be interested in the opinions/experiences of others who've tried it). I have a couple of questions: 1) Is it possible to automatically label just the calcarine itself? I know there is a pericalcarine label, but I am hoping to essentially label the line of the calcarine itself. 2) Is it possible to automatically find the occipital pole of the calcarine? The reason I want to do this is that it would then enable me to calculate the distance down the calcarine and the lateral distance away from the calcarine for each patch in the Hinds-V1 label. That potentially could be really useful in terms of sub-dividing the Hinds label into foveal and eccentric zones (although without retinotopy individual differences in M-scaling, for example, might limit interpretability). Would mris_divide_parcellation be useful here? Thanks in advance, Krish -- Prof. Krish Singh CUBRIC School of Psychology / Ysgol Seicoleg Cardiff University / Prifysgol Caerdydd Park Place / Plas y Parc Cardiff / Caerdydd CF10 3AT, UK Tel / Ffôn: 02920 874690 / 870365 Fax / Ffacs: 02920 870339 Email / Ebost : singhkd(a)cardiff.ac.uk

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freeview crash
by Hoptman, Matthew 08 Aug '11

08 Aug '11

Hi Ruopeg, No, glxgears doesn't crash. I'm getting about 3929 FPS. Thanks, Matt Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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FW: freeview crash
by Hoptman, Matthew 07 Aug '11

07 Aug '11

Hi all, I've been using Freesurfer for several years. I just upgraded to v. 5.1, but when I try to run freeview it crashes. I am running it on a 64-bit Centos 5.4 server and am accessing the server with Xming. When I try to start freeview it crashes Xming and I have to restart it. The only clue I have is when I try freeview.bin, I get "freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory". I'm wondering if it's a vtk problem. Any thoughts? --Matt Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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license file
by Hoptman, Matthew 06 Aug '11

06 Aug '11

Hi, I just registered my new installation of Freesurfer 5.1, but I've used 5.0 and 4.5 in the past. Can I just copy the ".license" file from the prior installation? My impression is I needed a new .license file for v. 5.1, but I haven't received it despite registering. --Matt Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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reference on co-registration of functional brain areas?
by Zeynep Akalin Acar 06 Aug '11

06 Aug '11

Hi all, I'm looking for a reference showing how the functional areas differ when individual brains are co-registered. Thanks, Zeynep.

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tksurfer and viewing eccentricity data
by Michelle Umali 05 Aug '11

05 Aug '11

Dear Freesurfers, Is this the correct command for viewing eccentricity data using tksurfer: tksurfer-sess -a rtopy.self.lh -s sj09 -map eccen Thanks. Michelle

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mri_segment optional flags problem
by Christopher Luna 05 Aug '11

05 Aug '11

Hello, I'm trying to run mri_segment with some custom values in the optional flags, such as -p for setting the percentage threshold with a float value. When I run the command though, "mri_segment -p 0.6 brain.mgz wm.seg.mgz" The command properly sets the threshold to 60%, but also takes the "0.6" to be in the input file name instead of brain.mgz. Is there another option I'm missing? Or have I unfortunately stumbled upon a small bug? Thanks, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT

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Nvidia upgrade considerations
by Andries R. Van Der Leij 05 Aug '11

05 Aug '11

Dear freesurfer team I'm currently investigating how to tweak 2 2 year old Dell 7400 Xeon machine's to run a large batch of fs jobs. Upgrading to Nehalem won't work, since it will require a new motherboard as well. However, we can replace our old non-fermi quadro card with a C2050. As an alternative, I was thinking about buying two GTX590 (two times 580 and 1.5 GB ram) or two palit GTX580 (1 times 580 with 3GB ram) and running them in SLI. This will save quite some money, and intuitively, it feels that more separate cards will work better if you start batching more recon scripts at the same time (1 per CPU). You'll end up with 6 gb of vram in both cases compared to the 3 for the C2050, with 4 processors for the 590 and 2 for the 580. As I don't understand cuda and sli well, I may very well be completely wrong. I'm not sure fi that running jobs under sli will work well. Do you have any ideas on this solution compared to a single c2050? thank you very much in advance, Andries van der Leij

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Error in preprocessing
by Eiran Vadim Harel 05 Aug '11

05 Aug '11

Hi, I am using stable5.0-env. I have run the pre[processing command: preproc-sess -s 1411_MC -surface fsaverage lhrh -mni305 -fwhm 5 -per-run I got this ERROR message: /autofs/space/shimshon_002/users/eiran/contproc/1411_MC RunList: 005 006 007 ------- ************************** ----------- ------- Motion Correcting Run 005 ----------- ------- ************************** ----------- sess = 1411_MC Fri Aug 5 11:51:17 EDT 2011 mc-afni2 --i 005/f.nii --t 005/template.nii --o 005/fmcpr.nii --mcdat 005/fmcpr.mcdat ERROR: cannot find AFNI command 3dvolreg My PROJECT DIR: /space/shimshon/2/users/eiran/contproc SUBJECTS_DIR: /space/shimshon/2/users/eiran/subjects Is there a way to solve it? Thanks, Eiran

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