[Freesurfer] Problems converting MNC to NII
Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar ___ 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] bvecs and bvals don't have the same number of entries
Hi everybody, I'm trying to run trac all -prep on my data but I'm getting this error bvecs and bvals don't have the same number of entries. I've checked my bvals and bvecs, which are in attach, but they seems to be formatted in the right way. The other 2 bvals and bvecs in DTI folder are the one saved by trac-all in the dmri directory. I'm attaching also my configuration file dmrirc.tutorial. Francesco Baldacchini dmrirc.tutorial Description: Binary data bvals Description: Binary data bvecs Description: Binary data bvals Description: Binary data bvecs 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] Problems converting MNC to NII
Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar ___ 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] dmri_motion Error bvals
Hi, Within the new Tracula update and with outputs resulted from *trac-all -prep -noqa* I ran *: * *dmri_motion --out './test.txt' --dwi './dwi_orig.nii.gz' --bval './bvals' --mat './dwi.ecclog'* And an error message appears: *machine x86_64Output motion measure file: /home/lapsi/test/motion.txtInput transform file: /home/lapsi/test/dwi.ecclogInput DWI file: /home/lapsi/test/dwi_orig.nii.gzInput b-value table: /home/lapsi/test/bvalsLow-b image intensity threshold: 100Nominal diffusivity: 0.001Loading volume-to-baseline affine transformationsComputing between-volume head motion measuresINFO: Processed transforms for 33 volumesLoading DWI volume series from /home/lapsi/test/dwi_orig.nii.gzLoading b-value table from /home/lapsi/test/bvalsERROR: Could not open /home/lapsi/test/bvals for reading* I tried with the b-values one value for each line in file bvalsT (see attachments): *dmri_motion --out 'teste.txt' --dwi 'dwi_orig.nii.gz' --bval './bvalsT' --mat 'dwi.ecclog'*,but the same error occurred. What can I do to verify this head motion? Thank you Best, -- Liliana Maia MEng Biomedical Engineering dwi.ecclog Description: Binary data bvals Description: Binary data bvalsT 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] Fwd: trac-all -path error
Hi Anastasia, I din't see anything missing from the brainmask or aparc+seg. I sent you the brainmask and aparc+seg files did you find anything wrong. if not, what else could cause the segmentatino fault? Thanks - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, January 10, 2014 6:15:23 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? Anything missing there that might affect the left ILF? a.y On Wed, 8 Jan 2014, Jon Wieser wrote: Dear freesurfer experts I'm getting the following error when runing trac-all -c dmrirc_single_subject -path Loading initial proposal SD's from /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt Processing pathway 3 of 18... Initializing MCMC Segmentation fault Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 I have attached the trac-all.log and trac-all.error files I am running tracula 5.3 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problems converting MNC to NII
Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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 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] Fwd: trac-all -prep error
Hi Anastasia, I didn't see anything blatently wrong with the apar+aseg or the DWI's. Can you be more specific as to what I should be looking for Thanks! Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, January 10, 2014 6:16:56 PM Subject: Re: [Freesurfer] Fwd: trac-all -prep error Hi Jon - Again I'd look at this subject's aparc+aseg, as well as the DWIs themselves to see if there's anything going on that might affect the left ILF. a.y On Wed, 8 Jan 2014, Jon Wieser wrote: Hello I'm getting the following error when running trac-all -c dmrirc -prep INFO: Distances between consecutive points in test subject's space are 7 9 7 8 WARN: Could not find satisfactory control point fit - try 809 Writing output files to /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1096/data/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_bbr_* Writing spline volume to /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1096/data/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_bbr_cpts_5.nii.gz Segmentation fault Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Wed Jan 8 12:07:54 CST 2014 i'm running traclua 5.3 attached are the trac-all.log and trac-ll.error files 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problems converting MNC to NII
how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problems converting MNC to NII
Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc ( http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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 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] Problems converting MNC to NII
Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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 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] Problems converting MNC to NII
Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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 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] Problems converting MNC to NII
can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar 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
Re: [Freesurfer] Problems converting MNC to NII
mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/ 32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar hmm, I don't know why that would be the case. Can you send the full command line and screen output? cheers Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The
Re: [Freesurfer] FreeSurfer installation
Hi Neda, Have you read over the linux install directions in the link below? You will need to register and get a license file. After that you should look over the setup and config instructions. https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration -Louis On Wed, 22 Jan 2014, Neda Mohammadi wrote: Hi dear all, I want to use freesurfer for tractography by FSL. I downloaded freesurfer-linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and I want to install it but I don't know how. Please help me. Thanks in advance, Neda ___ 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] Problems converting MNC to NII
same thing 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/ 32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the
[Freesurfer] Multiple Frames
Hello folks, I am attempting to run FreeSurfer (v5.1) on a downloaded NifTI structural T1 MRI from the Human Connectome Project, in particular 100307_3T_AFI.nii. Unless I am mistaken, their preprocessed data doesn't include aseg data, at least identified in a manner I am familiar with. Nevertheless, recon-all -s 100307_cs -all reports: ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/subjects/100307_cs/mri/orig/001.mgz has 2 frames. How do I work around this? Thanks, Al Alfred L. Ochs, Ph.D. Virginia Institute for Neuropsychiatry Richmond, Virginia ___ 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] Multiple Frames
p.s. thanks Matt Bruce On Wed, 22 Jan 2014, Glasser, Matthew wrote: AFI is a bias transmit scan, not an MPRAGE. Look for T1w. On 1/22/14 11:44 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Al, can you run mri_info on 100307_3T_AFI.nii? Is that an AFI scan? I'm not familiar with their naming convention. I'll cc Matt Glasser who can probably help. cheers Bruce On Wed, 22 Jan 2014, Alfred Ochs wrote: Hello folks, I am attempting to run FreeSurfer (v5.1) on a downloaded NifTI structural T1 MRI from the Human Connectome Project, in particular 100307_3T_AFI.nii. Unless I am mistaken, their preprocessed data doesn't include aseg data, at least identified in a manner I am familiar with. Nevertheless, recon-all -s 100307_cs -all reports: ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/subjects/100307_cs/mri/orig/001.mgz has 2 frames. How do I work around this? Thanks, Al Alfred L. Ochs, Ph.D. Virginia Institute for Neuropsychiatry Richmond, Virginia 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. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Multiple Frames
that's what I wondered. AFI = Actual Flip angle Imaging usually On Wed, 22 Jan 2014, Glasser, Matthew wrote: AFI is a bias transmit scan, not an MPRAGE. Look for T1w. On 1/22/14 11:44 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Al, can you run mri_info on 100307_3T_AFI.nii? Is that an AFI scan? I'm not familiar with their naming convention. I'll cc Matt Glasser who can probably help. cheers Bruce On Wed, 22 Jan 2014, Alfred Ochs wrote: Hello folks, I am attempting to run FreeSurfer (v5.1) on a downloaded NifTI structural T1 MRI from the Human Connectome Project, in particular 100307_3T_AFI.nii. Unless I am mistaken, their preprocessed data doesn't include aseg data, at least identified in a manner I am familiar with. Nevertheless, recon-all -s 100307_cs -all reports: ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/subjects/100307_cs/mri/orig/001.mgz has 2 frames. How do I work around this? Thanks, Al Alfred L. Ochs, Ph.D. Virginia Institute for Neuropsychiatry Richmond, Virginia 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. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problems converting MNC to NII
then is seems like the problem is with your mnc, not with anything we are doing, right? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: same thing 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii
Re: [Freesurfer] Problems converting MNC to NII
or, since the correct values display if I load the same MNC file with Matlab, it could be a problem with mri_binarize? 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu then is seems like the problem is with your mnc, not with anything we are doing, right? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: same thing 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/ 32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter
Re: [Freesurfer] Problems converting MNC to NII
and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I have tried the two following commands, and various flags on mri_convert: mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii Yhe output of the latter would be: mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from paxinos-MNI.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to paxinos-MNI.nii... for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference. It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than
Re: [Freesurfer] Multiple Frames
Hi Al, can you run mri_info on 100307_3T_AFI.nii? Is that an AFI scan? I'm not familiar with their naming convention. I'll cc Matt Glasser who can probably help. cheers Bruce On Wed, 22 Jan 2014, Alfred Ochs wrote: Hello folks, I am attempting to run FreeSurfer (v5.1) on a downloaded NifTI structural T1 MRI from the Human Connectome Project, in particular 100307_3T_AFI.nii. Unless I am mistaken, their preprocessed data doesn't include aseg data, at least identified in a manner I am familiar with. Nevertheless, recon-all -s 100307_cs -all reports: ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/subjects/100307_cs/mri/orig/001.mgz has 2 frames. How do I work around this? Thanks, Al Alfred L. Ochs, Ph.D. Virginia Institute for Neuropsychiatry Richmond, Virginia ___ 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] Problems converting MNC to NII
Can you describe the potential problem with mri_binarize more fully? On 01/22/2014 12:50 PM, Caspar M. Schwiedrzik wrote: or, since the correct values display if I load the same MNC file with Matlab, it could be a problem with mri_binarize? 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu then is seems like the problem is with your mnc, not with anything we are doing, right? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: same thing 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if
Re: [Freesurfer] Problems converting MNC to NII
Hi Doug, when I try to use mri_binarize with -match, certain values, especially ones smaller than about 50, are not found. This happens with the original MNC file as well as with NIFTI files that I converted from the MNC file. When I load the MNC file in Matlab, all the values that mri_binarize did not find show up. The data type of the MNC file is unsigned byte; it is read as 32bit integer in Matlab. Caspar 2014/1/22 Douglas N Greve gr...@nmr.mgh.harvard.edu Can you describe the potential problem with mri_binarize more fully? On 01/22/2014 12:50 PM, Caspar M. Schwiedrzik wrote: or, since the correct values display if I load the same MNC file with Matlab, it could be a problem with mri_binarize? 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu then is seems like the problem is with your mnc, not with anything we are doing, right? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: same thing 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu and what if you run it on the mnc? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu can you send us the full command line and screen output of the mri_binarize command? On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, I am confused, too. If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files? Caspar 2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu Hi Caspar now, I'm confused. So it sounds like mri_convert is doing the conversion properly then? Bruce On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: Hi Bruce, mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc ( http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255. The MNC is unsigned byte. Caspar
Re: [Freesurfer] FreeSurfer installation
Hi dear Louis, yes I read this link https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall but when I write this command setenv FREESURFER_HOME /usr/local/freesurfer I see this message: bash: setenv: command not found best, Neda On Wed, Jan 22, 2014 at 9:06 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Neda, Have you read over the linux install directions in the link below? You will need to register and get a license file. After that you should look over the setup and config instructions. https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration -Louis On Wed, 22 Jan 2014, Neda Mohammadi wrote: Hi dear all, I want to use freesurfer for tractography by FSL. I downloaded freesurfer-linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and I want to install it but I don't know how. Please help me. Thanks in advance, Neda 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 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] Cortical Flat Mapping Crash
h, I'm not sure then. Maybe some version of open GL? Perhaps Nick or Zeke can comment? On Wed, 22 Jan 2014, Sherryse Corrow wrote: Hi Bruce, Our system is Centos 6. We can try it on another system today, although we don't have another system that is as fast/efficient as our Centos 6 machine. Sherryse ___ 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] Multiple Frames
BTW: If you download the structural preprocessed data, the HCP data already includes aparc+aseg.nii.gz in both native space and transformed to MNI152 space. If you want the data values contained in the native space aseg.stats file of FreeSurfer, you can quickly get that as part of the spreadsheet of data available for each subject at db.humanconnectome.org cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 1/22/14 11:47 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: that's what I wondered. AFI = Actual Flip angle Imaging usually On Wed, 22 Jan 2014, Glasser, Matthew wrote: AFI is a bias transmit scan, not an MPRAGE. Look for T1w. On 1/22/14 11:44 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Al, can you run mri_info on 100307_3T_AFI.nii? Is that an AFI scan? I'm not familiar with their naming convention. I'll cc Matt Glasser who can probably help. cheers Bruce On Wed, 22 Jan 2014, Alfred Ochs wrote: Hello folks, I am attempting to run FreeSurfer (v5.1) on a downloaded NifTI structural T1 MRI from the Human Connectome Project, in particular 100307_3T_AFI.nii. Unless I am mistaken, their preprocessed data doesn't include aseg data, at least identified in a manner I am familiar with. Nevertheless, recon-all -s 100307_cs -all reports: ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/subjects/100307_cs/mri/orig/001.mgz has 2 frames. How do I work around this? Thanks, Al Alfred L. Ochs, Ph.D. Virginia Institute for Neuropsychiatry Richmond, Virginia 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. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] surface repositioning tool documentation
Hi, Is there documentation for the use of freeview's surface repositioning tool? Including the recon-all steps that should be rerun to ensure that the surface edits are reflected in the surface stats? Are edits made with this tool applied to future runs through the recon-all process (like pial and wm edits)? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755 ___ 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] FreeSurfer installation
Hi Neda, Your terminal is probably setup to use the bash environment by default. If you type tcsh, then you'll be using C shell and that command should then work. I see that this is not on the install page, but on the setup/config page there is a note about it. There are also alternate commands to use for bash if you want on that page as well. -Louis On Wed, 22 Jan 2014, Neda Mohammadi wrote: Hi dear Louis, yes I read this link https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall but when I write this command setenv FREESURFER_HOME /usr/local/freesurfer I see this message: bash: setenv: command not found best, Neda On Wed, Jan 22, 2014 at 9:06 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Neda, Have you read over the linux install directions in the link below? You will need to register and get a license file. After that you should look over the setup and config instructions. https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration -Louis On Wed, 22 Jan 2014, Neda Mohammadi wrote: Hi dear all, I want to use freesurfer for tractography by FSL. I downloaded freesurfer-linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and I want to install it but I don't know how. Please help me. Thanks in advance, Neda 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 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] Problems converting MNC to NII
I've looked at the volume you sent. One problem may be that the minc
file might have a scale factor which we are not properly reading. When I
use mnc2nii it produces a nifti file that has a slope of 1.00392. Not
much, but it is there. The values that come out are not integer and
there is nothing in the range of 0-73. Using loadminc.m I can see values
in the range of 0-73. The datafile has slice-dependent scaling (based on
what loadminc is doing). We don't rescale by slice when loading minc. I
would suggest finding a program that does the correct rescaling. One
possibility is to first do the conversion with mri_convert to create
junk.nii the in matlab
a = MRIread('junk.nii');
[imaVOL,scaninfo] = loadminc('paxinos-MNI.mnc');
a.vol = imaVOL;
MRIwrite(a,'myvol.nii');
doug
On 01/22/2014 01:09 PM, Caspar M. Schwiedrzik wrote:
Hi Doug,
when I try to use mri_binarize with -match, certain values, especially
ones smaller than about 50, are not found.
This happens with the original MNC file as well as with NIFTI files
that I converted from the MNC file.
When I load the MNC file in Matlab, all the values that mri_binarize
did not find show up.
The data type of the MNC file is unsigned byte; it is read as 32bit
integer in Matlab.
Caspar
2014/1/22 Douglas N Greve gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
Can you describe the potential problem with mri_binarize more fully?
On 01/22/2014 12:50 PM, Caspar M. Schwiedrzik wrote:
or, since the correct values display if I load the same MNC file
with
Matlab, it could be a problem with mri_binarize?
2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
then is seems like the problem is with your mnc, not with
anything
we are doing, right?
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
same thing
2014/1/22 Bruce Fischl fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
and what if you run it on the mnc?
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
mri_binarize --i paxinos-MNI.nii --match 1 --o
labels/1.nii
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08
15:40:50
greve Exp $
cwd
/rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque
cmdline mri_binarize --i paxinos-MNI.nii
--match 1
--o labels/1.nii
sysname Linux
hostname wiener
machine x86_64
user cschwiedrz
input paxinos-MNI.nii
frame 0
nErode3d 0
nErode2d 0
output labels/1.nii
Binarizing based on matching values
nMatch 1
0 1
binval1
binvalnot 0
Found 0 values in range
Counting number of voxels
Found 0 voxels in final mask
mri_binarize done
2014/1/22 Bruce Fischl
fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
can you send us the full command line and
screen output of the
mri_binarize command?
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik
wrote:
Hi Bruce,
I am confused, too.
If the conversion is proper, why
does
mri_binarize
not find values below
~53? when I call mri_binarize with
-match on the MNC
file or on any of the
converted NIFTI files?
Caspar
2014/1/22 Bruce Fischl
fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
mailto:fis...@nmr.mgh.harvard.edu
Re: [Freesurfer] glm specification in longitudinal analyses for one group
Hi Sandra, so you reduce the 2 thickness measures within subject to a rate of change (mm/time), then you have a single map for each subject and now your question is about your glm modeling. So the question is basically about cross sectional modeling in you GLM. Your equ 7 and 8 test if there is an overall effect (thinning or thickening) not considering any co-variates. Your other three models 1,3,5 include different amounts of covariates in the model. Of course you will get different results as you are basically 'regressing out' these variables, when placing a zero in the contrast. The variables are used to build the model and fit the functions, but not for the testing. Now let's look at model 5. You have two groups, scanner 1 and scanner 2. The constrast [1 1] tests if the rate in group 1 plus the rate in group 2 is different from zero. In order to better interpret the gamma map, I'd probably do [ 0.5 0.5 ] to have gamma show the average rate between these two groups, sig won't change. You could also test [ 1 -1 ] to test if there is a difference between the groups (to see if the scanner has an effect on the atrophy rates, assuming groups are matched, or when including (regressing out) appropriate co-variates such as age, gender, etc). So to answer your question: the different models should not give the same results as they test different things. If you get very different results by including / removing a co-variable, that may mean that that variable is important for your analysis. There is a large body of work on parameter selection. I am not a statistician, so not the best person to discuss this with. Hope my explanations already help. Best, Martin On 01/22/2014 05:40 AM, Sandra Preissler wrote: Dear freesurfer experts and users At the moment our group is working on longitudinal analyses for two different time points in one group. Our analyses worked well and we tried to calculate the effects of six different covariates and one fix moderator variable (we had two different MRI Scanner and tried to consider this effect) with the function mri_glmfit. We did pre-processing with mri_preproc: mris_preproc --fsgd extra_komplett.fsgd --cache-in long.thickness-rate.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.extra_komplett.thickness.10.mgh With the fsgd-File designed like the following example: GroupDescriptorFile 1 Title G1V2 Class Scannertyp-Main Variables z1 z2 z3 z4 z5 z6 Input P01 Scannertyp-Main T3 z11 z21 z31 z41 z51 z61 ... Because of the consideration of the variable Scanner we designed the design matrix on our own. Before calculating the effect of the covariates we calculated the main effect (for the assumed underlying regression model please refer to equation number 1 in the attached pdf). For doing this we built a contrast file (please refer to equation 2). In a longer discussion we decided to delete different covariates and get the regression model shown in equation 3 (and the contrast file for the main effect in equation 4). Surprisingly both main effects not even were similar. Therefore we tried two different models (please refer to equation 5 and 7 for the two regression models). If the underlying model is a normal linear model the first three Contrasts and regression models should gave the same results. In our analyses we have really different results, therefore we have problems in interpreting and understanding the underlying general linear model. There seems to be still an influence of the covariates even if there are modeled with 0 (which in our understanding means they were mathematically not included in the model). Is the probability dependent on the distribution of the covariates even if they are modeled with no influence? If so, how is the belonging regression model? The information about the freesurfer version and linux version used are: FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Kernel info: Linux 2.6.34.10-0.6-default x86_64 Can you help us in fixing this theoretical problem? Thanks in advance! Sandra This message was sent through https://webmail.uni-jena.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is
