Re: [Freesurfer] Dev builds not found
Thanks! It's working now! On Sunday, September 18, 2016 10:34 PM, Leila Reddy <le...@yahoo.com> wrote: Hi Bruce,Thanks for your reply. Does anyone on the list have access to the tar file of the latest dev build that they could put on some other site or in a public Dropbox folder? I totally changed my system and don't have a working version of Freesurfer/FS-FAST anymore and am pretty much stuck. Otherwise, do you think I should try to install an older version of perl? Sorry to cause you trouble,Thanks, Leila ___ 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.
Re: [Freesurfer] Dev builds not found
Hi Bruce,Thanks for your reply. Does anyone on the list have access to the tar file of the latest dev build that they could put on some other site or in a public Dropbox folder? I totally changed my system and don't have a working version of Freesurfer/FS-FAST anymore and am pretty much stuck. Otherwise, do you think I should try to install an older version of perl? Sorry to cause you trouble,Thanks, Leila___ 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] Dev builds not found
Hi,I get an error with mri_nu_correct.mni. I've seen on the FS wiki that this is because I have a new version of perl and that I should download the development version. However, I cannot access this page ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ (nothing happens on a linux machine, and I get a 550 Failed to change directory error on a Mac). Is there another place I can download the fixed version from? Thanks,Leila ___ 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.
Re: [Freesurfer] convert from MNI152 to native space
Hi FS Experts, I'm trying to use the mni152reg command but I get an error that --lta is not recognized. It appears that fslregister doesn't have this option. There was a previous post about this problemhttp://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41953.html but I can't figure out if the problem had been solved. The version of mni152reg I am using is$Id: mni152reg,v 1.9 2014/07/07 18:59:08 greve Exp $ on Mac OS 10.8. Thanks,Leila On Wednesday, June 15, 2016 11:55 AM, Leila Reddy <le...@yahoo.com> wrote: Hi, I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to convert this mask into the native space of each subject. I tried the following command but the results do not look right in Freeview: mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o mask_in_Native.nii --mni152reg The overlay of the mask on f.nii in Freeview is mostly outside the brain. How can I go about this step? Thanks for your help,Leila ___ 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.
Re: [Freesurfer] convert from MNI152 to native space
Hi Doug, Thanks for your reply. When I run mni152reg I get an error : ERROR: Flag --lta unrecognized I'm using v 1.9 of this file. I found a post that said to download a newer version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg but it doesn't seem to be there anymore. Thanks, Leila On Wednesday, June 15, 2016 11:55 AM, Leila Reddy <le...@yahoo.com> wrote: Hi, I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to convert this mask into the native space of each subject. I tried the following command but the results do not look right in Freeview: mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o mask_in_Native.nii --mni152reg The overlay of the mask on f.nii in Freeview is mostly outside the brain. How can I go about this step? Thanks for your help,Leila ___ 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] convert from MNI152 to native space
Hi, I have a binary mask from the WFU_Pickatlas. I think this mask in in the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 109 91]. I would like to convert this mask into the native space of each subject. I tried the following command but the results do not look right in Freeview: mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o mask_in_Native.nii --mni152reg The overlay of the mask on f.nii in Freeview is mostly outside the brain. How can I go about this step? Thanks for your help,Leila ___ 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] Question about selxavg3-sess -no-con-ok
Hi,I was just wondering what exactly the -no-con-ok option does in selxavg3-sess. Is it the same as setting the weights for all conditions to 1 and give the baseline/fixation (i.e., 0s in the para files) a weight of 0? Thanks, Leila ___ 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.
Re: [Freesurfer] help with save_nifti
Hi Doug, Thanks for your reply. I have the problem even if I use MRIread and MRIwrite. But I have done a little more digging following your suggestions. Basically, there are differences in the output of mri_vol2surf (that I should have spotted earlier), as well as differences in the header information. I highlight the differences below, and I have put the detailed outputs of mri_vol2surf at the end in case you still need to look at it. I think the clearest way of explaining the different outcomes is as follows.: 1) mri_vol2surf performed on a nifti volume generated by Nibabel. Nothing done in Matlab. mri_vol2surf ouput: Number of source voxels hit = 22587. niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm Results looks fine in tksurfer (i.e., I have a distribution of voxel values in the Configure Overlay window). If I look at the nifti header, hdr.volres= [2.e+10 2.e+10 2.e+10] and several other fields (e.g., vox2ras etc) also have the same magnitude. In addition, hdr.niftihdr.dim'=[3 76 76 93 1 1 1 1] 2) The Nibabel nifti is opened in matlab with MRIread and immediately saved with MRIwrite. Nothing else is done to the data in Matlab. Output of MRIread=WARNING: xyz units code 0 is unrecognized Rescaling NIFTI: slope = 1, intercept = 0 mri_vol2surf output: Number of source voxels hit = 1. Nothing about NIFTI_UNITS (note the header is the same as in 1 above). Rest of mri_vol2surf output is exactly as for #1 above. The header values are as above except hdr.niftihdr.dim'=[4 76 76 93 1 1 1 1] 3) The Nibabel nifti is opened in matlab with MRIread. The 3d volume is saved with MRIwrite but with the header information from a FSFAST created nifti. mri_vol2surf says Number of source voxels hit = 22587. hdr.volres=[2 2 2] and other fields have values of the same order. hdr.niftihdr.dim'=[4 76 76 93 1 1 1 1] I don't know if I have focused on the relevant header information here so I also attach the headers from steps 1-3 above. Thanks a lot for your help and time on this. I will often have to go back and forth between python functions and Matlab/FS-FAST scripts so this will be very useful. Leila Detailed output of mri_vol2surf with fsfast header (#3 above): mri_vol2surf --src fs_hdr.nii --hemi rh --out_type mgh --float2int round --o fshdr-rh.mgh --projfrac 0.5 --trgsubject fsaverage --regheader fsaverage srcvol = fs_hdr.nii srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /APPLICATIONS/freesurfer/subjects/fsaverage/mri/orig.mgz as target reference. Reading surface /APPLICATIONS/freesurfer/subjects/fsaverage/surf/rh.white Done reading source surface Reading thickness /APPLICATIONS/freesurfer/subjects/fsaverage/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 22587 Writing to fshdr-rh.mgh Dim: 163842 1 1 Detailed output of mri_vol2surf with nibabel header (after opening and saving in matlab) (#2 above): mri_vol2surf --src test.nii --hemi rh --out_type mgh --float2int round --o test-rh.mgh --projfrac 0.5 --trgsubject fsaverage --regheader fsaverage srcvol = test.nii srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /APPLICATIONS/freesurfer/subjects/fsaverage/mri/orig.mgz as target reference. Reading surface /APPLICATIONS/freesurfer/subjects/fsaverage/surf/rh.white Done reading source surface Reading thickness /APPLICATIONS/freesurfer/subjects/fsaverage/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 1 Writing to test-rh.mgh Dim: 163842 1 1 hdrs.mat Description: application/matlab-workspace ___ 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] help with save_nifti
Hi,
I am trying to save a nifti file using save_nifti. I'm running into a strange
problem that I describe below.
I have a nifti file (subj_mask.nii) created by a colleague using Nibabel
(http://nipy.sourceforge.net/nibabel/). This volume is in the MNI305 space.
Step1: In a first step I wanted to convert this volume to the fsaverage surface
format. To do that I used :
mri_vol2surf --src subj_mask.nii --hemi rh --out_type mgh --float2int round
--o blah9-rh.mgh --projfrac 0.5 --trgsubject fsaverage --regheader fsaverage.
I load it in tksurfer and when I do view- configure-overlay, I see a range of
values (as expected) and am able to set the min and max thresholds as I want.
Step 2: In a second step I loaded this nifti file into matlab using load_nifti
and had to alter the volume a little bit as below:
hdr=load_nifti('subj_mask.nii');
vol=hdr.vol;
vol(find(vol4))=0;
hdr.vol=vol;
save_nifti(hdr,'new_mask.nii').
I convert the volume to fsaverage surface space as before but when I view it in
tksurfer I am not able to set a min and max threshold with configure-overlay.
Instead, there is no distribution of values plotted in the configure overlay
window and I get the following error message: % ERROR updating histo:
impossible limits (min 0.6 = max 0.6) for axis x
I finally managed to solve this problem by loading the header information from
a FS-FAST created nifti:
hdr_fsfast = load_nifti('bold/analysis.mni/mask.nii.gz');
hdr_fsfast.vol=vol;
save_nifti(hdr_fsfast,'new_mask.nii').
Now I am able to see the distribution of values in the configure overlay window
and am able to set the thresholds.
The headers for FS-FAST and Nibabel generated niftis are indeed slightly
different but why do I not have the problem in step 1 when I use the Nibabel
file, but only in step 2 after I use save_nifti with the Nibabel header ?
I use the load_nifti and save_nifti commands very often (and haven't had
problems before because I was only using FS-FAST generated files) so I would
really appreciate it if someone could point out what is going on so that I
understand what to do in future.
Thanks,
Leila___
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[Freesurfer] Question about freesurfer coordinates
Hi, I've been trying to understand the FScoordinates powerpoint and I would like to ask a few questions (these questions might simply be about mri_convert, depending on where my confusion is...). 1) I think the orig.mgz volume is in the CRS space. Now, looking at slide 8 in the powerpoint, if I want to go from a point in orig.mgz (CRS) to the corresponding point in MNI305 (CRS), I would have to do: inv(Nb)*X*Na*my_point. However, to get the whole volume from orig.mgz to MNI305, the following command does the job: mri_convert orig.mgz --apply_transform transforms/talariach.xfm -oc 0 0 0 orig.talairach.mgz. Does this step automatically include the Na and inv(Nb) operations? Or am I wrong about the starting spaces for orig.mgz and MNI305? 2) I get the same result as above for the talairach transform if I use: mri_convert --apply_transform transforms/talariach.xfm --devolvexfm subjectid -ic 0 0 0 orig talairach. I see now what devolvexfm is, but which space in the flowchart on slide 8 is it operating on? -ic and -oc seem to be important because I don't get the same results if I use -ic for the first command and -oc for the second command, but I don't find any documentation on what exactly these options do. Thanks, Leila ___ 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.
Re: [Freesurfer] Question about preproc-sess -no-subcort-mask
Hi Doug, Here it is. cheers, Leila From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Leila Reddy le...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 1, 2013 5:53 PM Subject: Re: Question about preproc-sess -no-subcort-mask Hmmm, not sure what to say. CAn you send me $FREESURFER_HOME/fsfast/bin/preproc-sess ? On 10/01/2013 07:45 AM, Leila Reddy wrote: Hi Doug, I don't think that could have happened as I only found out about the no-subcort-mask option yesterday (after I had done all the original analysis). I have just re-run all the analyses for the same subject with the same commands on the two machines (output of bugr for the 2 machines is below). I had deleted everything from this subject's bold directory except the f.nii and para.para files for each run, so that everything is re-analyzed. I get the same problem as before. I attach a screen capture of freeview with my bold/analysis.mni/mask.nii overlaid on freesurfer/average/mni305.cor.mgz from the two machines. As you can see, they are different. They only look the same if I re-run the analysis on snowleopardv5.3.0 with preproc-sess -no-subcort-mask. Thanks again, Leila Machine 1: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Kernel info: Darwin 10.8.0 i386 - Machine 2: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.0.0 x86_64 - Date: Mon, 30 Sep 2013 17:48:15 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question about preproc-sess -no-subcort-mask To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 5249f19f.3070...@nmr.mgh.harvard.edu mailto:5249f19f.3070...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed They do have the same default. Note that if you run preproc-sess with -no-subcort-mask and then run it again without -no-subcort-mask it will not generate a new file. Could that have happened? doug -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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. preproc-sess Description: Binary data ___ 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.
Re: [Freesurfer] Question about preproc-sess -no-subcort-mask
Hi Doug, Now that I know that I wasn't inadvertently making a stupid mistake in my analysis, and I also know how to get around the problem, I don't really need to solve it anymore. Thanks for your time. Leila From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Leila Reddy le...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 1, 2013 6:57 PM Subject: Re: Question about preproc-sess -no-subcort-mask I have to say that I'm stumped. Do you really need to resolve this question? doug On 10/01/2013 12:27 PM, Leila Reddy wrote: Hi Doug, Here it is. cheers, Leila *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Leila Reddy le...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Tuesday, October 1, 2013 5:53 PM *Subject:* Re: Question about preproc-sess -no-subcort-mask Hmmm, not sure what to say. CAn you send me $FREESURFER_HOME/fsfast/bin/preproc-sess ? On 10/01/2013 07:45 AM, Leila Reddy wrote: Hi Doug, I don't think that could have happened as I only found out about the no-subcort-mask option yesterday (after I had done all the original analysis). I have just re-run all the analyses for the same subject with the same commands on the two machines (output of bugr for the 2 machines is below). I had deleted everything from this subject's bold directory except the f.nii and para.para files for each run, so that everything is re-analyzed. I get the same problem as before. I attach a screen capture of freeview with my bold/analysis.mni/mask.nii overlaid on freesurfer/average/mni305.cor.mgz from the two machines. As you can see, they are different. They only look the same if I re-run the analysis on snowleopardv5.3.0 with preproc-sess -no-subcort-mask. Thanks again, Leila Machine 1: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Kernel info: Darwin 10.8.0 i386 - Machine 2: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.0.0 x86_64 - Date: Mon, 30 Sep 2013 17:48:15 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question about preproc-sess -no-subcort-mask To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 5249f19f.3070...@nmr.mgh.harvard.edu mailto:5249f19f.3070...@nmr.mgh.harvard.edu mailto:5249f19f.3070...@nmr.mgh.harvard.edu mailto:5249f19f.3070...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed They do have the same default. Note that if you run preproc-sess with -no-subcort-mask and then run it again without -no-subcort-mask it will not generate a new file. Could that have happened? doug -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https
[Freesurfer] Question about preproc-sess -no-subcort-mask
Hi, I would like to verify (as a sanity check and to make sure that I'm on the right track in my analysis) that preproc-sess runs with -no-subcort-mask by default in freesurfer-Darwin-lion-stable-pub-v5.2.0, but with -no-subcort-mask turned off by default in stablev5.3.0 on snowleopard. I first did an MNI305 analysis in v5.2.0 (mountain lion) and was able to see my slices very nicely overlaid on the average/mni305.cor.mgz brain. However, the same analysis in v5.3.0 (snowleopard) didn't overlay on the brain in a sensible way, and only after I searched the mailing list did I realize that I needed to use -no-subcort-mask. Using this option gave me the same results as with v.5.2.0. Searching through freesurfer/fsfast/bin/preproc-sess I don't see where this flag is set by default to -no-subcort-mask in v5.2.0 (in fact, it seems that ApplySubCortMask = 1; by default). So I'm pretty confused, and I'm just not sure that I'm doing things the right way... Thanks in advance, Leila ___ 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.
Re: [Freesurfer] Question about preproc-sess -no-subcort-mask
Hi again, Sorry, I didn't list all the commands I have been using: preproc-sess -s $subj -fsd bold -sliceorder odd -surface fsaverage lhrh -mni305 -fwhm 3 -per-run -force (and with -no-subcort-mask in v5.3.0 on snowleopard) mkanalysis-sess -fsd bold -stc odd -mni305 2 -fwhm 3 -paradigm para.para -nconditions 5 -gammafit 2.25 1.25 -TR 2 -analysis analysis-sm3.mni -event-related -refeventdur 2 -polyfit 1 -mcextreg -per-run -rlf runlist -timeoffset -1.0 -refeventdur 2 -force mkcontrast-sess -analysis analysis-sm3.mni -contrast visresp -a 1 -c 2 selxavg3-sess -s $subj -analysis analysis-sm3.mni Then I look at the mask.nii created in bold/analysis-sm3.mni overlaid on mni305.cor.mgz (I view the overlay with freeview). The overlaid mask.nii from v5.3.0 looks the same as mask.nii from v5.2.0 only if I use -no-subcort-mask in v5.3.0. Leila Hi, I would like to verify (as a sanity check and to make sure that I'm on the right track in my analysis) that preproc-sess runs with -no-subcort-mask by default in freesurfer-Darwin-lion-stable-pub-v5.2.0, but with -no-subcort-mask turned off by default in stablev5.3.0 on snowleopard. I first did an MNI305 analysis in v5.2.0 (mountain lion) and was able to see my slices very nicely overlaid on the average/mni305.cor.mgz brain. However, the same analysis in v5.3.0 (snowleopard) didn't overlay on the brain in a sensible way, and only after I searched the mailing list did I realize that I needed to use -no-subcort-mask. Using this option gave me the same results as with v.5.2.0. Searching through freesurfer/fsfast/bin/preproc-sess I don't see where this flag is set by default to -no-subcort-mask in v5.2.0 (in fact, it seems that ApplySubCortMask = 1; by default). So I'm pretty confused, and I'm just not sure that I'm doing things the right way... Thanks in advance, Leila___ 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.
Re: [Freesurfer] error with fast_selxavg3
Hi Doug, Thanks for your reply. Yes, it does work with a longer -refeventdur. In fact, I had tried that yesterday before posting my original message but I'd forgotten to make the corresponding changes to the 3rd column of the paradigm file and so kept getting the error message. The shortest I can bring -refeventdur down to is 0.05. Anything smaller causes the same error as before. In the end it's not a huge problem for us if we have to set an event duration of 50ms instead of 16.6 ms but I'd like to understand what is going on. So, I wondered if the error had anything to do with the fact that when I run mkcontrast-sess the script automatically sets -TER to 0.05. I re-ran the analysis and set -TER and -refeventdur to 0.016 in mkanalysis-sess. The analysis runs with no error for selxavg-sess and visually (with tksurfer) the results look the same as with -TER and -refeventdur set to 0.05. Since the help for mkanalysis-sess -TER says It is best to know what you are doing if you are going to change this., I'd like to know if it makes sense to change the TER like I have. What does the TER achieve (if that's not too complicated a question)? Thanks again, Leila ___ 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] error with fast_selxavg3
Hi, I am running into an error with fast_selxavg3 (NaN values in XtX). Other have people reported similar problems on the mailing list and I've tried implementing some of the suggestions (namely, using -nowhiten and checking that all events exist in my paradigm file), but I can't get rid of the error. I have an event-related design with very short events (duration of 1 screen refresh = 16.6ms) presented at random intervals. The error only occurs for the -gammafit and -spmhrf analyses and not for -fir. When I check the Xtmp.mat there are indeed NaNs in the first 2 columns of the X matrix. The commands I issue and the output of bugr are below.I attach the paradigm file from one run of the experiment (there are 5 runs in all but I started focusing on just one in order to troubleshoot). TR=2 and numTRs=172. Any help would be much appreciated. Thanks in advance, Leila mkanalysis-sess -fsd bold -surface fsaverage lh -fwhm 3 -event-related -paradigm VRpara.para -nconditions 1 -gammafit 2.25 1.25 -TR 2 -refeventdur 0.016 -polyfit 2 -mcextreg -analysis TargDist-gammafit-sm3.lh -per-run -rlf runlist -force -nowhiten mkcontrast-sess -analysis TargDist-gammafit-sm3.lh -contrast VR -a 1 selxavg3-sess -s $subj -analysis TargDist-gammafit-sm3.lh Error message: - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /APPLICATIONS/freesurfer/fsfast/toolbox/fast_selxavg3.m /APPLICATIONS/freesurfer/fsfast/toolbox/fast_ldanaflac.m /APPLICATIONS/freesurfer/matlab/MRIread.m - outtop = /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF Extension format = nii.gz 1 VR.mat nruns = 1 autostimdur = outanadir = /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh Found 149786/163842 (91.4) voxels in mask Creating Design Matrix ... creation time = 0.005 sec DoMCFit = 1 ntptot = 172, nX = 7, DOF = 165 Saving X matrix to /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 36) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); -- ERROR: fast_selxavg3() failed\n Output of bugr: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.0.0 x86_64 - VRpara.para Description: Binary data ___ 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] Download problem wih freesurfer-Darwin-lion-stable-pub-v5.2.0.dmg
Hi, I'm trying to install the latest Mac OSX 64bit FreeSurfer version but when I click on the download link I get an error: 550 Failed to change directory. I can't find a file with this filename in ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ either. Is this version not yet available (and when will it be available)? Thanks, Leila ___ 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.
Re: [Freesurfer] selxavg error
Hi Doug,
I couldn't find a -no-whiten option in the usage for either selxavg-sess or
selxavg3-sess. In any case, when I run the selxavg command, the screen output
says:
INFO: WhitenFlag = 0 (so I guess it's not whitening?).
I also looked for spikes or artifacts as you suggested and the main thing that
struck me is that for the two subjects for whom I get this error, the min value
in the 4D vol is 0 whereas for the 2 subjects that don't have this error, the
min(vol) is non-zero (negative values in one subject and non-zero, positive for
the other). Otherwise the amplitude profiles look pretty similar for all
subjects. Could this be a divide by zero error somewhere in selxavg? And is
there some way around it?
Thanks in advance,
Leila
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Leila Reddy le...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Fri, March 12, 2010 8:12:54 PM
Subject: Re: [Freesurfer] selxavg error
hmmm, something is going wrong with the whitening. Can you try it without
whitening? Also, look in the 4d volume for some artifact (eg, a spike). This
might account for it.
doug
Leila Reddy wrote:
Hi,
I'm running into an error with selxavg ('Input to SVD must not contain NaN or
Inf') that has been posted before on the mailing list but I couldn't find a
solution to it.
The command was selxavg-sess -sf sessid -df sessdir -analysis loc-sm3. The
output of the log file is:
selxavg-sess log file
$Id: selxavg-sess,v 1.15 2006/01/06 02:37:22 greve Exp $
uid=502(lreddy) gid=502(lreddy) groups=502(lreddy), 81(appserveradm),
79(appserverusr), 80(admin)
/Volumes/donnees/GR/gr_analysis/kan_gr_006
/Applications/freesurfer/fsfast/bin/selxavg-sess
-sf sessid -df sessdir -analysis loc-sm3
Darwin g5-leila.local 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10
18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386
Fri Mar 12 17:07:53 CET 2010
selxavg: Command not found.
---
/Volumes/donnees/GR/gr_data/kan_gr_006
Fri Mar 12 17:07:53 CET 2010
/Volumes/donnees/GR/gr_data/kan_gr_006/bold
selxavg2 -TR 2. -parname loc.para -o loc-sm3/h -i 018/fmc-sm3 -i
019/fmc-sm3 -i 020/fmc-sm3 -cfg
/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg -ipr 1.40625
-pomnibus loc-sm3/omnibus/fsig -fomnibus loc-sm3/omnibus/f
cat: /Applications/freesurfer/fsfast/docs/version: No such file or directory
--- Parsing Config File:
/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg
-gammafit 2.25 1.25 -timewindow 30 -prestim 6 -polyfit 1 -TER 2 -nskip 0
-fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000
Logfile is loc-sm3/h_sxa.log
matlab file is /tmp/sxa_5739.m
--- Matlab file --
% Matlab file for selxavg2 Fri Mar 12 17:07:53 CET 2010
% This file may be deleted
% /tmp/sxa_5739.m
global QuitOnError;
QuitOnError = 1;
r = fast_selxavg( '-TR', '2.', '-parname', 'loc.para', '-o', 'loc-sm3/h',
'-i', '018/fmc-sm3', '-i', '019/fmc-sm3', '-i', '020/fmc-sm3', '-cfg',
'/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg', '-ipr',
'1.40625', '-pomnibus', 'loc-sm3/omnibus/fsig', '-fomnibus',
'loc-sm3/omnibus/f');
if(r==0)
fmri_touch('/Volumes/donnees/GR/gr_data/kan_gr_006/bold/loc-sm3/selxavg.ok.5739');
end
qoe;
---
--
--- matlab output
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
M A T L A B
Copyright 1984-2007 The MathWorks, Inc.
Version 7.4.0.287 (R2007a)
January 29, 2007
Warning: Duplicate directory name: /Users/lreddy/matlab.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.comhttp://www.mathworks.com.
$Id: fast_selxavg.m,v 1.22.2.2 2006/09/29 21:54:40 greve
Exp $
Parsing Arguments
RescaleTarget = 1000
Checking Parameters
AutoStimDur: 0
StimDur: Number of Runs: 3
Input Volume List
1 018/fmc-sm3
2 019/fmc-sm3
3 020/fmc-sm3
Input Pardigm File List
1 018/loc.para
2 019/loc.para
3 020/loc.para
Output Volume loc-sm3/h
F Omnibus Volume loc-sm3/omnibus/f
Sig Omnibus Volume loc-sm3/omnibus/fsig
TR2.00
TER 2.00
Total Window 30
PreStim Window 6
Remove Baseline 1
Remove Trend0
Remove QTrend 0
Rescale Target 1000
nSkip 0
InPlane Res 1.40625
FWHM0
Hanning Radius 0
Time Offset 0
GammaFit1
1 2.25 1.25
GammaFit Alpha: 2
SPM HRF: -1
Seg Brain/Air 1
SynthSeed 0
ExtReg File mcextreg
NExtReg 3
[Freesurfer] selxavg error
Hi,
I'm running into an error with selxavg ('Input to SVD must not contain NaN or
Inf') that has been posted before on the mailing list but I couldn't find a
solution to it.
The command was selxavg-sess -sf sessid -df sessdir -analysis loc-sm3.
The output of the log file is:
selxavg-sess log file
$Id: selxavg-sess,v 1.15 2006/01/06 02:37:22 greve Exp $
uid=502(lreddy) gid=502(lreddy) groups=502(lreddy), 81(appserveradm),
79(appserverusr), 80(admin)
/Volumes/donnees/GR/gr_analysis/kan_gr_006
/Applications/freesurfer/fsfast/bin/selxavg-sess
-sf sessid -df sessdir -analysis loc-sm3
Darwin g5-leila.local 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28
PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386
Fri Mar 12 17:07:53 CET 2010
selxavg: Command not found.
---
/Volumes/donnees/GR/gr_data/kan_gr_006
Fri Mar 12 17:07:53 CET 2010
/Volumes/donnees/GR/gr_data/kan_gr_006/bold
selxavg2 -TR 2. -parname loc.para -o loc-sm3/h -i 018/fmc-sm3 -i
019/fmc-sm3 -i 020/fmc-sm3 -cfg
/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg -ipr 1.40625
-pomnibus loc-sm3/omnibus/fsig -fomnibus loc-sm3/omnibus/f
cat: /Applications/freesurfer/fsfast/docs/version: No such file or directory
--- Parsing Config File:
/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg
-gammafit 2.25 1.25 -timewindow 30 -prestim 6 -polyfit 1 -TER 2 -nskip 0 -fwhm
0 -extreg mcextreg -nextreg 3 -rescale 1000
Logfile is loc-sm3/h_sxa.log
matlab file is /tmp/sxa_5739.m
--- Matlab file --
% Matlab file for selxavg2 Fri Mar 12 17:07:53 CET 2010
% This file may be deleted
% /tmp/sxa_5739.m
global QuitOnError;
QuitOnError = 1;
r = fast_selxavg( '-TR', '2.', '-parname', 'loc.para', '-o', 'loc-sm3/h',
'-i', '018/fmc-sm3', '-i', '019/fmc-sm3', '-i', '020/fmc-sm3', '-cfg',
'/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg', '-ipr',
'1.40625', '-pomnibus', 'loc-sm3/omnibus/fsig', '-fomnibus',
'loc-sm3/omnibus/f');
if(r==0)
fmri_touch('/Volumes/donnees/GR/gr_data/kan_gr_006/bold/loc-sm3/selxavg.ok.5739');
end
qoe;
---
--
--- matlab output
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
M A T L A B
Copyright 1984-2007 The MathWorks, Inc.
Version 7.4.0.287 (R2007a)
January 29, 2007
Warning: Duplicate directory name: /Users/lreddy/matlab.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
$Id: fast_selxavg.m,v 1.22.2.2 2006/09/29 21:54:40 greve Exp $
Parsing Arguments
RescaleTarget = 1000
Checking Parameters
AutoStimDur: 0
StimDur: Number of Runs: 3
Input Volume List
1 018/fmc-sm3
2 019/fmc-sm3
3 020/fmc-sm3
Input Pardigm File List
1 018/loc.para
2 019/loc.para
3 020/loc.para
Output Volume loc-sm3/h
F Omnibus Volume loc-sm3/omnibus/f
Sig Omnibus Volume loc-sm3/omnibus/fsig
TR2.00
TER 2.00
Total Window 30
PreStim Window 6
Remove Baseline 1
Remove Trend0
Remove QTrend 0
Rescale Target 1000
nSkip 0
InPlane Res 1.40625
FWHM0
Hanning Radius 0
Time Offset 0
GammaFit1
1 2.25 1.25
GammaFit Alpha: 2
SPM HRF: -1
Seg Brain/Air 1
SynthSeed 0
ExtReg File mcextreg
NExtReg 3
ExtRegOrthog 0
firstslice 0
nslices 17
nyqreg 0
SynthSeed = 0
Conditions Found (4): 1 2 3 4
Run 1: 32 32 32 32
Run 2: 32 32 32 32
Run 3: 32 32 32 32
Slice 0, 9.3119e-05 --
First Pass (Accumulation), 0.000414148
Run 1/3, 0.000853017
Excluding 0 Points:
Run 2/3, 0.622743
Excluding 0 Points:
Run 3/3, 1.0841
Excluding 0 Points:
Second Pass (Residual Error Estimation), 1.52296
??? Error using == svd
Input to SVD must not contain NaN or Inf.
Error in == cond at 40
s = svd(A);
Error in == fast_selxavg at 193
c = cond(SumXtWX);
??? Undefined function or variable 'r'.
quiting matlab
2010-03-12 17:08:05.047 MATLAB[5789] Process manager already initialized --
can't fully enable headless mode.
--
ERROR: fast_selxavg() failed\n
The output of bugr is
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5
Kernel info: Darwin 8.11.1 i386
Thanks in advance,
Leila
___
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
[Freesurfer] inorm-sess error
Hi, I'm trying to get around the problems from my previous post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07669.html I am now trying to use mri_convert to convert from nifti to bshort using the following command: mri_convert -i rfkoch-0021-00144-000144-00.nii -it nii -o fspm2_000.bshort -ot bshort The bshort files seem to be created but then when I run inorm-sess I get the following error. The odd thing is that when I used mri_concat on exactly the same .nii files (as mentioned in my previous post) I was able to run inorm-sess with no errors... What is the difference between these two commands? The inorm error: Warning: Matrix is singular to working precision. In fast_inorm at 196 ??? Error using == betainc at 35 X must be in the interval [0,1]. The exact output from the command is pasted below. Here is the output of bugr: - FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5 Kernel info: Darwin 8.11.1 i386 - If anyone has any suggestions I'd be grateful to hear them! Thanks! inorm-sess -sf sessid -df sessdir -rlf runlist_inormcheck -funcstem fspm2 /Volumes/donnees/Imagery/imagery_data/RF005 Thu Jun 19 17:43:17 CEST 2008 Filesystem 512-blocks Used Avail Capacity Mounted on /dev/disk0s3 808067040 465870224 34219681658%/Volumes/donnees RunList 021 -- /Volumes/donnees/Imagery/imagery_data/RF005/bold inorm -i 021/fspm2 -umask 22 -TR 2. -ipr 3 -bpr 2.998958184 -seqname PerImg -- Log file is 021/inorm.log inorm matlab file is /tmp/inorm_21280.m --- Matlab file -- %%% - %% % matlab file to run inorm % This is a temporary file and may be deleted % /tmp/inorm_21280.m global QuitOnError; QuitOnError = 1; r = fast_inorm( '-i', '021/fspm2', '-umask', '22', '-TR', '2.', '-ipr', '3', '-bpr', '2.998958184', ' ', 'PerImg'); quit; --- -- --- matlab output Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. M A T L A B Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.287 (R2007a) January 29, 2007 Warning: Duplicate directory name: /Users/lreddy/matlab. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. $Id Parsing Arguments Checking Parameters invol021/fspm2 firstslice 0 nslices 32 relthresh0.75 reportfile 021/fspm2.report meanvalfile 021/fspm2.meanval twfstem 021/fspm2.twf TR 2.00 First Pass: Computing global mean 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Second Pass: Segmenting 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Warning: Matrix is singular to working precision. In fast_inorm at 125 Warning: Matrix is singular to working precision. In fast_inorm at 146 Warning: Matrix is singular to working precision. In fast_inorm at 175 Warning: Matrix is singular to working precision. In fast_inorm at 196 ??? Error using == betainc at 35 X must be in the interval [0,1]. Error in == tTest at 37 p = betainc(z,dof/2,0.5); Error in == fast_inorm at 223 tSigCor = tTest(s.ntp-2,tCor); 2008-06-19 17:43:31.661 MATLAB[21307] Process manager already initialized -- can't fully enable headless m ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] orientation problem when converting from SPM .nii format to bshort
Hi, I am trying to convert SPM5 .nii files into bshort and I used the following command: mri_concat fkoch-0007*.nii --o bold/007/fspm_000.bshort The command seems to work in that I have a bunch of bshort files in my bold/007 directory but when I try to view the slices (using sliceview-sess for example) the slices are all upside-down (rotated by 180 degrees). Is there an option I can use to get them the right side up? I'm using FS v3 on an IntelMac and my version of mri_concat is stable3. Here is the output of bugr: - FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5 Kernel info: Darwin 8.11.1 i386 - Thanks, Leila ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Error with selxavg-sess
Hi,
I encountered an error with selxavg-sess -sf sessid -df sessdir -analysis
loc-sm3. Looking through the archives I found that others had errors with
selxavg-sess but the errors don't seem to be exactly the same as mine.
Please let me know if you have any suggestions on how to get this to work.
My log file is pasted at the bottom of this email.
I use the PowerPC version of freesurferv4.0.1
-
FREESURFER_HOME: /Software/freesurfer
Build stamp: freesurfer-Darwin-tiger-stable-pub-v4.0.1
Kernel info: Darwin 8.10.0 Power Macintosh
-
Thanks a lot!
Leila
selxavg-sess log file
$Id: selxavg-sess,v 1.18 2007/01/09 22:41:18 nicks Exp $
uid=1132(lreddy) gid=1132(lreddy) groups=1132(lreddy), 1185(kraskov),
1152(rodri), 1090(psycho)
/Users/lreddy/Desktop/Leila-Data/Imagery/imagery_analysis/RSK006
/Software/freesurfer/fsfast/bin/selxavg-sess
-sf sessid -df sessdir -analysis loc-test
Darwin wagner.klab.caltech.edu 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10
18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc
Sun Nov 18 20:20:37 PST 2007
selxavg: Command not found.
---
/Users/lreddy/Desktop/Leila-Data/Imagery/imagery_data/RSK006
Sun Nov 18 20:20:37 PST 2007
/Users/lreddy/Desktop/Leila-Data/Imagery/imagery_data/RSK006/bold
selxavg2 -TR 2. -parname loc.para -o loc-test/h -i 011/f -i 021/f -i 025/f
-cfg
/Users/lreddy/Desktop/Leila-Data/Imagery/imagery_analysis/RSK006/loc-test/analysis.cfg
-ipr 3 -pomnibus loc-test/omnibus/fsig -fomnibus loc-test/omnibus/f
here
--- Parsing Config File:
/Users/lreddy/Desktop/Leila-Data/Imagery/imagery_analysis/RSK006/loc-test/analysis.cfg
-gammafit 2.25 1.25 -timewindow 30 -prestim 6 -polyfit 1 -TER 2 -nskip 0 -fwhm 0
-extreg mcextreg -nextreg 3 -rescale 1000
Logfile is loc-test/h_sxa.log
matlab file is /tmp/sxa_6634.m
--- Matlab file --
% Matlab file for selxavg2 Sun Nov 18 20:20:38 PST 2007
% This file may be deleted
% /tmp/sxa_6634.m
global QuitOnError;
QuitOnError = 1;
r = fast_selxavg( '-TR', '2.', '-parname', 'loc.para', '-o', 'loc-test/h',
'-i', '011/f', '-i', '021/f', '-i', '025/f', '-cfg',
'/Users/lreddy/Desktop/Leila-Data/Imagery/imagery_analysis/RSK006/loc-test/analysis.cfg',
'-ipr', '3', '-pomnibus', 'loc-test/omnibus/fsig', '-fomnibus',
'loc-test/omnibus/f');
if(r==0)
fmri_touch('/Users/lreddy/Desktop/Leila-Data/Imagery/imagery_data/RSK006/bold/loc-test/selxavg.ok.6634');
end
exit
qoe;
---
--
--- matlab output
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
Warning:
MATLAB is starting without a display, using internal event queue.
You will not be able to display graphics on the screen.
M A T L A B
Copyright 1984-2006 The MathWorks, Inc.
Version 7.2.0.283 (R2006a)
January 27, 2006
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Warning: Duplicate directory name: /home/lreddy/matlab.
In path at 113
In startup at 380
In matlabrc at 216
$Id: fast_selxavg.m,v 1.40 2007/01/15 02:29:36 greve Exp $
Parsing Arguments
RescaleTarget = 1000
UseMRIread = 1, ext = bhdr
Checking Parameters
nslices = 32
AutoStimDur: 0
StimDur:
Number of Runs: 3
Input Volume List
1 011/f
2 021/f
3 025/f
Input Pardigm File List
1 011/loc.para
2 021/loc.para
3 025/loc.para
Output Volume loc-test/h
F Omnibus Volume loc-test/omnibus/f
Sig Omnibus Volume loc-test/omnibus/fsig
TR2.00
TER 2.00
Total Window 30
PreStim Window 6
Remove Baseline 1
Remove Trend0
Remove QTrend 0
Rescale Target 1000
nSkip 0
InPlane Res 3
FWHM0
Hanning Radius 0
Time Offset 0
GammaFit1
1 2.25 1.25
GammaFit Alpha: 2
SPM HRF: -1
Seg Brain/Air 1
SynthSeed 0
ExtReg File mcextreg
NExtReg 3
ExtRegOrthog 0
firstslice 0
nslices 32
nyqreg 0
SynthSeed = 0
Conditions Found (4): 1 2 3 4
Run 1: 32 32 32 32
Run 2: 32 32 32 32
Run 3: 32 32 32 32
Slice 0, 9.29485e-05 --
First Pass (Accumulation), 0.000672511
Run 1/3, 0.00150713
Excluding 0 Points:
Warning: Divide by zero.
In fast_selxavg at 440
Loading 011/f
Run 2/3, 3.50438
Excluding 0 Points:
Warning: Divide by zero.
In fast_selxavg at 440
Loading 021/f
Run 3/3, 6.90937
Excluding 0 Points:
Warning: Divide by zero.
In fast_selxavg at 440
Loading 025/f
Second Pass
