[Freesurfer] "preproc-sess" failing at 3dvolreg
Hi, I am trying to analyze my fMRI data ( collected at MGH) using FSFAST and I was following the tutrial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastWorkFlows). I was able to unpack the data. But when I run "preproc-sess -s -fwhm 2", it fails at 3dvolreg. Here is the log file fmc.nii.mclog. I checked the tempvol.nii.gz . afni was able to open it and disply the slice. Any help is welcome. regards, krishna /tmp/sk/FSFAST/abe_090116/bold /usr/local/imports/freesurfer/fsfast/bin/mc-afni2 --i 005/f.nii --t 005/f.nii --frame 0 --o 005/fmc.nii --mcdat 005/fmc.mcdat Thu Jan 22 19:07:38 EST 2009 uid=2308(sk) gid=12308(sk) groups=11(floppy),17(audio),18(video),19(cdrom),12308(sk),12345(spm),12349(numbra) ives Linux ives 2.6.24.5-smp #2 SMP Wed Apr 30 13:41:38 CDT 2008 i686 Intel(R) Xeon(R) CPU E5405 @ 2.00GHz GenuineIntel GNU/Linux /usr/local/imports/freesurfer/bin/3dvolreg mcdat file is 005/fmc.mcdat tmp dir is 005/tmp.mc-afni2.15217 #...@# /tmp/sk/FSFAST/abe_090116/bold mri_convert 005/f.nii 005/tmp.mc-afni2.15217/tempvol.nii.gz --nskip 0 --ndrop 160 -odt float mri_convert 005/f.nii 005/tmp.mc-afni2.15217/tempvol.nii.gz --nskip 0 --ndrop 160 -odt float nskip = 0 ndrop = 160 $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from 005/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.34202, -0.939693) k_ras = (-0, -0.939693, 0.34202) changing data type from 4 to 3 (noscale = 0)... Dropping last 160 frames writing to 005/tmp.mc-afni2.15217/tempvol.nii.gz... #...@# /tmp/sk/FSFAST/abe_090116/bold mri_convert 005/f.nii 005/tmp.mc-afni2.15217/invol.nii.gz -odt float mri_convert 005/f.nii 005/tmp.mc-afni2.15217/invol.nii.gz -odt float $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from 005/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.34202, -0.939693) k_ras = (-0, -0.939693, 0.34202) changing data type from 4 to 3 (noscale = 0)... writing to 005/tmp.mc-afni2.15217/invol.nii.gz... #...@# /tmp/sk/FSFAST/abe_090116/bold 3dvolreg -verbose -dfile 005/fmc.mcdat -base 005/tmp.mc-afni2.15217/tempvol.nii.gz -prefix 005/tmp.mc-afni2.15217/outvol.nii.gz 005/tmp.mc-afni2.15217/invol.nii.gz ++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [32-bit] ++ Authored by: RW Cox ** ERROR (nifti_image_read): failed to find header file for '005/tmp.mc-afni2.15217/tempvol.nii.gz' ** Couldn't open -base dataset 005/tmp.mc-afni2.15217/tempvol.nii.gz ERROR: 3dvolreg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] memory alloc problem in mri_fwhm
Hi, I am analyzing my fMRI data and I got a memory alloc problem in "mri_fwhm" The exact message is : mri_fwhm --mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii --i /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/res/all.nii --sum /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.sum --dat /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.dat MRIalloc(96, 84, 33): could not allocate 32256 bytes for 12483th slice voxelvolume 3.1901 mm3 Loading mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii Search region is 84788 voxels = 270482.522603 mm3 Polynomial detrending, order = 0 Detrending Cannot allocate memory I am using the binaries from "freesurfer-Linux-rh9-stable-pub-v4.0.5". I am pretty new to FSFAST. Any pointers will be helpful. regards, Krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] memory alloc problem in mri_fwhm
Hi, "all.nii" takes 1309 MB. I have 4 GB RAM and a 80 GB HDD. regards, Krishna Douglas N Greve wrote: how big is all.nii and how much memory do you have on that computer? Krishna Srihasam wrote: Hi, I am analyzing my fMRI data and I got a memory alloc problem in "mri_fwhm" The exact message is : mri_fwhm --mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii --i /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/res/all.nii --sum /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.sum --dat /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.dat MRIalloc(96, 84, 33): could not allocate 32256 bytes for 12483th slice voxelvolume 3.1901 mm3 Loading mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii Search region is 84788 voxels = 270482.522603 mm3 Polynomial detrending, order = 0 Detrending Cannot allocate memory I am using the binaries from "freesurfer-Linux-rh9-stable-pub-v4.0.5". I am pretty new to FSFAST. Any pointers will be helpful. regards, Krishna ___ 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] Error while registering functionals to anatomicals
Hi, I am getting an error if I try to register my functionals to anatomical image (using spmregister-sess command). It is looking for file 'subjectname'. Here are the steps I did before coming across this error. Did I miss anything? step 1 : unpacking data (unpacksdcmdir command) step 2 : run motion correction (preproc-sess command) step 3: created the paradigm file step 4: registering functional to anatomical /** spmregister-sess -s abe_090116 -- spmregister-sess logfile is /tmp/sk/FSFAST/log/spmregister-sess.19224.log -- Session: /tmp/sk/FSFAST/abe_090116 Wed Jan 28 13:27:34 EST 2009 ERROR: file 'subjectname' does not exist in /tmp/sk/FSFAST/abe_090116 /** regards, Krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] using old GE data to run FSFAST
Hi, I have some fMRI data which i collect from GE signa 3T machine. I have the data in two formats : (1) IMA format ( where each run is a directory like "01.SER" and each such directory has separate files for each acquisition i.e. if I had 150 acquisitions, I have 150 .IMA files (2) I also have the above-mentioned data in nifti format exactly like before..Separate directories for each runs and separate files for each acquisition. Is there any command or way to convert these files into a format that I can use to do analysis with FSFAST. regards, Krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] averaging fMRI data across multiple scan sessions
Hi, We had collected a lot of data in our first few scan sessions trying different TR/TE/voxel size/REPs combinations in order to get the optimal values. Now, I would like to do a joint analysis of all those scans. Is it possible ? regards, Krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] aligning functionals to anatomicals
Hi, I have a question regarding overlay of functional activations on a freesurfer map. After much work, I flattened my monkey brain. But, I just realized that the input volume , which I used to generate the flat maps, had orientation set to LIA. I want to over lay my functional activations, which are in RAS orientation on them. One way would be to realign all functional data into LIA orientation and then analyze the data and then simply use spmregister-see or fslregister-sess to register. Is there any simpler way? My functionals are 65x85x56 for each slice. I tried using flirt to get the alignment matrix. But, it is failing badly.. Any ideas would be welcome.. Regards, krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] isxconcat-sess question..
Hi, Is there a way to use" isxconcat-sess" to average monkey fMRI data? i.e. I have two groups of monkeys (say, test and control groups) and I want to do group analysis on their data.. Regards, krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
