[Freesurfer] cannot allocate memory problem when using make average subject
Hi, I was trying to build an average subject using 250 subjects and I got the following error message: processing subject nor76 (246 of 250) reading spherical surface /DATA_FREESURFER/Data/nor76/surf/rh.sphere.reg... reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) curvature mean = -0.017, std = 0.597 curvature mean = -0.064, std = 0.640 ripping medial wall... computing parameterization for surface /DATA_FREESURFER/Data/nor76/surf/rh.inflated.H... ImageAlloc: could not allocate 512x256 buffer curvature mean = -0.088, std = 0.872 Cannot allocate memory I saw someone discussing this issue a few month ago and Doug provided new scripts of make_average_subject, make_average_volume and make_average_surface to solve this problem. However, I can't find these files using the link ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ Can anyone tell me whether and how this problem has been solved? Thanks in advance! Jiefeng Jiang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all times
Re: [Freesurfer] recon-all timesHi everybody, Here is the results from my server: CPU-MODEL: 2 x Intel(R) Xeon(R) E5320 CPU-FREQ: 1.86GHz RAM: 12GB HD-type: SATA FREESURFER-VERSION:freesurfer-Linux-rh9-stable-pub-v4.0.1-full.tar.gz OS: Ubuntu 7.10 Processing-TIME: 29.5h for the subject bert - Original Message - From: Juergen Haenggi To: Thomas Doering ; Freesurfer Mailinglist Sent: Thursday, January 17, 2008 3:41 PM Subject: Re: [Freesurfer] recon-all times Hi Thomas, hi FS users Here are the data from my MacPro QuadCore (Mac OS X 10.4) CPU-MODEL: 2 x Intel(R) Xeon(R) CPU-FREQ: 2.66GHz RAM: 7GB HD-type: SATA (Serial ATA) Chip-Set: NVIDIA GeForce 7300 GT FREESURFER-VERSION TIME: freesurfer-Darwin-tiger-i686-stable-pub-v4.0.1-full.dmg Processing-TIME: 24.25 h for the subject bert Best regards Juergen On 15.1.2008 13:32 Uhr, "Thomas Doering" <[EMAIL PROTECTED]> wrote: CPU-MODEL: 2 x Intel(R) Xeon(R) CPU X5355 CPU-FREQ: 2.66GHz RAM: 16GB FREESURFER-VERSION TIME: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 TIME: 20.5 h --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [EMAIL PROTECTED] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) --- -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] vertex neighbourhood
If you want to write your own program to do this, you can use the ANN lib at http://www.cs.umd.edu/~mount/ANN/ - Original Message - From: <[EMAIL PROTECTED]> To: Sent: Friday, January 25, 2008 5:02 AM Subject: [Freesurfer] vertex neighbourhood > hi surfers, > Imagine that I need to know what are the closest N vertices (let's say > n=100) to a given vertex (i mean two dimentionsal neighourhood on > surfaces) . Any idea how to do that? anybody has a written code for this? > cheers > nima > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] A problem with Deflate compression of tif format
Hi, I met the problem of "Deflate compression support is not configured. TiffWrite: TIFFWriteScanline returned error" when I used mris_make_template. Currently I use libtiff4 for tiff interface and zlib1g for deflate compression. In addition, I linked libtiff.so.3 to libtiff.so.4. I also tested the two libs by opening and saving a sample tiff image and they worked well. I have no idea how to solve this, maybe I need to establish another link for deflate compression... Could somebody give me some advices? Thank you in advance! Jiefeng Jiang Medical image computing National lab of pattern recognition Institute of automation, CAS Beijing, China +86 10 62659278___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How to generate inflated.H file?
Hi, Happy New Year everybody! I met a problem when I tried to make a template using "mris_make_template", it needs ?h.inflated.H file. However, I only have ?h.inflated file. Does anyone know how to generate ?h.inflated.H file? Thank you in advance! Jiefeng Jiang Medical image computing National lab of pattern recognition Institute of automation, CAS Beijing, China +86 10 62659278___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How to register a subject surface to average surface?
Hi, I used make_average_subject to create an average subject, and I want to register a subjects's pial surface to the average subject's pial surface. I used mris_make_template lh pial average lh.pial.tif to create a template, and used mris_register -curv lh.pial $SUBJECTS_DIR/average/surf/lh.pial.tif lh.pial.avg.reg but the result was a sphere. Could anyone tell me how to do the registration? Thank you in advance! Jiefeng Jiang Medical image computing National lab of pattern recognition Institute of automation, CAS Beijing, China +86 10 62659278 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Average surface of mris_register
Sorry that I did not make it claer. The resampling did not fail, just the result was not good. The resamping process is like this: I treated reconstructed cortical surfaces as functions defined on a sphere. Meanwhile, I divided a sphere into 163842 points and 300,000+ triangles by iteratively subdividing a icosahedron for 7 times. I would like to compute the spatial coordinates of the 163842 points in R^3 space and then get a resampled cortical surface. To achieve this, I linearly interpolated the 163842 points on the ?h.sphere.reg files and computed their spatial positions. The problem is that after spherical registration, the triangles on ?h.sphere.reg became more unevenly distributed(or distorted) -- some of them had very small areas. Thus the 163842 points which were evenly spread on the sphere may not resample all the details of the cortical surface. In my case, some resampled triangles were too large that some sulci disappeared. I hope that changing the default average surface of mris_register may fix the problem... Thanks. - Original Message - From: "Bruce Fischl" <[EMAIL PROTECTED]> To: "Jiefeng Jiang" <[EMAIL PROTECTED]> Cc: Sent: Thursday, September 20, 2007 7:45 PM Subject: Re: [Freesurfer] Average surface of mris_register > I'm sorry, I don't understand. What resampling fails? How does it fail? > > On > Thu, 20 Sep 2007, Jiefeng Jiang wrote: > >> Hi, >> >> I am using the ?h.sphere.reg files automatically generated by reconall. >> However, I found that the area distortion compromise the results of my >> following resample step. I wonder whether replacing the default average >> surface "$FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif" >> with the ?h.sphere in the /average/surf directory would reduce the >> distortion. If so, could anyone tell me how to get a .tif file using files >> in /average/surf directory? >> >> Thank you! >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Average surface of mris_register
Hi, I am using the ?h.sphere.reg files automatically generated by reconall. However, I found that the area distortion compromise the results of my following resample step. I wonder whether replacing the default average surface "$FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif" with the ?h.sphere in the /average/surf directory would reduce the distortion. If so, could anyone tell me how to get a .tif file using files in /average/surf directory? Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
