Re: [Freesurfer] surface lines in manual edits
Thanks Lee. I'll see how this works. I hope these examples make me an expert too. Best, Jennifer -Original Message- From: Lee Tirrell [mailto:ltirr...@nmr.mgh.harvard.edu] Sent: Saturday, August 29, 2015 5:50 PM To: Kriegel, Jennifer Lynn Sarai Cc: Freesurfer support list Subject: RE: [Freesurfer] surface lines in manual edits Hi Jennifer, The mri_segment command only creates a volume file that is similar to wm.mgz, it doesn't reproduce the surfaces. You can think of it like a command that adds or removes voxels from the wm.mgz based on intensity values in the brain.mgz (or whatever image you give it as input; brain.mgz is the volume recon-all uses for wm segmentation). Since your original wm.mgz file covered almost the entire brain (original_wm.jpg), I clicked around and noticed that the intensity values for what should be grey matter were much higher in your brain.mgz (up to around 100, when they're usually in the 70s) I tried a few different wlo values, and visually inspected the resulting file in freeview to see how it looks. For example (see attached wlo-105_wm.jpg for screenshot): mri_segment -wlo 105 brain.mgz test_wm.mgz freeview brainmask.mgz test_wm.mgz:colormap=heat:opacity=0.2 This test_wm.mgz looks much better than your original wm.mgz, so I figured this would be a good value to use for your expert options. From there, I just ran the recon-all command with the expert.opts file (see recon-all_xprt-opts.jpg for screenshot of results): recon-all -autorecon2-wm -autorecon3 -expert /path/to/expert.opts -s subject_name with the expert.opts file containing these two lines: mri_segment -wlo 105 mris_make_surfaces -wlo 105 I didn't test out the mris_make_surfaces command, I just used the same wlo value as for mri_segment as Bruce suggested since mris_make_surfaces also uses an intensity value to find the border between white matter and gray matter. The white surfaces are based off of the wm.mgz so if the results of mri_segment with your wlo value looks good, the surfaces with that wlo value should also be improved. Since the results of re-running recon-all looked pretty good, I didn't try changing more parameters. If you wanted to try this yourself, the command recon-all uses is this (change lh to rh to do the right hemisphere): mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs -wlo 105 subject_name lh You can run mris_make_surfaces --help for more info, and look at the scripts/recon-all.cmd file for the exact command that recon-all used (the recon-all.log file also contains the commands and all terminal output). These commands take longer to run than mri_segment, and only do one hemi at a time. Hope this puts you on a path to becoming a Freesurfer expert. Best, Lee On Sat, 29 Aug 2015, Kriegel, Jennifer Lynn Sarai wrote: Hi Lee, I’m replying to the list on this, in case anyone else echoes this trouble when altering surfaces. In addition to the email help, I also checked the thread noted, which specified that the recon-all.log file would have the line information. I followed the mri folder commands you offered, both as more recent, as well as the fact that the recon-all.log file listed a mean, not a solid min/max number. I’ve been trying to play around with the command options you gave me, so that the other two brains that had this problem at the initial reconstruction can also be adjusted, and I know what I’m doing. When I ran this command: mri_segment -wlo 105 brain.mgz 105_o01.mgz it produced a file, but I can’t tell how the normalization intensity is from the file set up, and I ended up with no segment lines. Hence the second command line, I’m sure… However, some of this makes sense to me on this, and some doesn’t. There’s a segment.dat file in the MRI folder, and thus it runs the adjustment command on the brain.mgz file. There is no make_surfaces.dat file. I figured I’d run the command for the fun of it: mris_make_surfaces -wlo 105 brain.mgz 105_o01.mgz – using brain.mgz because of the instructions you’d given me to run the commands from the mri folder, and assuming the logic that both commands were altering the brain.mgz file. and got told there was no brain.mgz subject in my directory: /home/jlk130230/anatomical/brain.mgz/mri/filled.mgz was the volume that couldn’t be opened. So, I moved back out to my subject directory for this, based on both the error and the wiki information on the command, using: mris_make_surfaces -wlo 105 fmri35_o01 r l 105_o01.mgz based on the wiki information to use the subject, then input information on hemispheres, and the volume to be altered. This time, I thought maybe that it needed to alter the 105_o01 file I’d created with the segment command, since that was the dat file that was located in the folder. However, first – unlike the instructions on the wiki stated, the hemisphere information was not recognized, it was seen
Re: [Freesurfer] surface lines in manual edits
Hi Lee, I’m replying to the list on this, in case anyone else echoes this trouble when altering surfaces. In addition to the email help, I also checked the thread noted, which specified that the recon-all.log file would have the line information. I followed the mri folder commands you offered, both as more recent, as well as the fact that the recon-all.log file listed a mean, not a solid min/max number. I’ve been trying to play around with the command options you gave me, so that the other two brains that had this problem at the initial reconstruction can also be adjusted, and I know what I’m doing. When I ran this command: mri_segment -wlo 105 brain.mgz 105_o01.mgz it produced a file, but I can’t tell how the normalization intensity is from the file set up, and I ended up with no segment lines. Hence the second command line, I’m sure… However, some of this makes sense to me on this, and some doesn’t. There’s a segment.dat file in the MRI folder, and thus it runs the adjustment command on the brain.mgz file. There is no make_surfaces.dat file. I figured I’d run the command for the fun of it: mris_make_surfaces -wlo 105 brain.mgz 105_o01.mgz – using brain.mgz because of the instructions you’d given me to run the commands from the mri folder, and assuming the logic that both commands were altering the brain.mgz file. and got told there was no brain.mgz subject in my directory: /home/jlk130230/anatomical/brain.mgz/mri/filled.mgz was the volume that couldn’t be opened. So, I moved back out to my subject directory for this, based on both the error and the wiki information on the command, using: mris_make_surfaces -wlo 105 fmri35_o01 r l 105_o01.mgz based on the wiki information to use the subject, then input information on hemispheres, and the volume to be altered. This time, I thought maybe that it needed to alter the 105_o01 file I’d created with the segment command, since that was the dat file that was located in the folder. However, first – unlike the instructions on the wiki stated, the hemisphere information was not recognized, it was seen as a file name: /home/jlk130230/anatomical/fmri35_o01/surf/r.orig: could not open file No such file or directory So, I got rid of the hemisphere information, and ran it without that – mris_make_surfaces -wlo 105 fmri35_o01 105_o01.mgz This time, I realized there is no surf folder that is recognized based on the file name - /home/jlk130230/anatomical/fmri35_o01/surf/105_o01.mgz.orig does not exist. The surf file is outside of the mri folder, and also contains no dat file with the mris_make_surfaces command, and the mri folder has a brainfinalsurfs.mgz file – but, it doesn’t seem like this would help edit the new volume either, nor is it specifically surf. While searching the wiki on expert opts, I found Bruce’s notice on some commands being designed to be sure that experts were using them – which I’m sure I’m not – but, do you think you can point me in the right direction on this Thanks very much! Jennifer Kriegel -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Lee Tirrell Sent: Friday, August 28, 2015 4:06 PM To: Freesurfer support list Subject: Re: [Freesurfer] surface lines in manual edits After taking a look through some of these subjects, it appears there is low contrast between white and gray matter. The gray matter has higher intensity than what is normally expected by Freesurfer. Re-running the subjects with expert options that raise the lower intensity threshold for white matter greatly improves the result (although further edits to wm.mgz may also be necessary). The command would be: recon-all -autorecon2-wm -autorecon3 -expert /path/to/expert.opts -s subject_name The expert.opts files contains these two lines: mri_segment -wlo 105 mris_make_surfaces -wlo 105 If you want to play around with how these expert options are working, you can run the command below from your subject's mri directory (it is quick). This is the command that makes the first guess at wm.mgz. By default, wlo is 90, but since the gm is so bright, it needs to be raised so that only voxels with intensity 105 are considered wm. I tried a few different values and looked at the output_file.mgz in freeview before settling on 105 for your subject. mri_segment -wlo num brain.mgz output_file.mgz A previous thread with the subject how to shrink wm surface gives some further detail from Bruce and others. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37990.html Best, Lee On Mon, 24 Aug 2015, Bruce Fischl wrote: Hi Jennifer sorry for the lack of response - do you want to upload your subject data (the entire subject directory) and we will take a look? cheers Bruce On Mon, 24 Aug 2015, Kriegel, Jennifer Lynn Sarai wrote: Hi, I apologize for asking this question again, but I’m still
Re: [Freesurfer] surface lines in manual edits
Hi Freesurfer experts, I asked this question yesterday. I ended up seeing that a similar question had been asked in July, and spoke to the asker of the question, who told me his problem had been zeroes on the control point dat file, for several points. I have attempted to go back through these, and reran several subjects with such zeroes removed, however - the same problem reoccurs with the white matter surface being seen as the brain surface. Any help would be welcomed. Thank you. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Kriegel, Jennifer Lynn Sarai Sent: Wednesday, August 19, 2015 10:44 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] surface lines in manual edits Hi, I'm hand editing brains to get the most accurate cortical thickness analysis possible, and ran into a bit of a problem with surface lines. One issue is with the original structural reconstructions from the hdr files, and the other deals with the manual edits I've made when the recon was re-run. 1. A couple of the volumes initially had the white matter surface as the pial surface/cortical surface. Initially I tried running g-cut for some of the suggestions I found on the wiki when the surface lines are off. This didn't work on those problem volumes. 2. When editing with control points in order to get the white matter areas that were not incorporated into the white matter surface included, the control points have overcoverected and made the same issue that was the occurrence with the two or three original volumes - the white matter surface is seen as the brain/pial surface. I was conservative with these as well. I have been looking on the wiki for a way to adjust the actual surface lines manually based on the actual white matter/brain surface. I think this would be most useful, but I'm not sure if it is possible. If so, how could this be done - and, if not, what possible way of trouble shooting can help deal with this white matter as pial surface issue? Best regards, - Jennifer Lynn Sarai Kriegel MS in Psychological Sciences, Cognition and Neuroscience Emphasis Functional Neuroimaging of Memory Lab, Center for Vital Longevity The University of Texas at Dallas jlk130...@utdallas.edumailto:jlk130...@utdallas.edu I am looking for a lot of men who have an infinite capacity to not know what can't be done. - Henry Ford The important thing is not to stop questioning. Curiosity has its own reason for existing. - Albert Einstein ___ 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] surface lines in manual edits
Hi, I'm hand editing brains to get the most accurate cortical thickness analysis possible, and ran into a bit of a problem with surface lines. One issue is with the original structural reconstructions from the hdr files, and the other deals with the manual edits I've made when the recon was re-run. 1. A couple of the volumes initially had the white matter surface as the pial surface/cortical surface. Initially I tried running g-cut for some of the suggestions I found on the wiki when the surface lines are off. This didn't work on those problem volumes. 2. When editing with control points in order to get the white matter areas that were not incorporated into the white matter surface included, the control points have overcoverected and made the same issue that was the occurrence with the two or three original volumes - the white matter surface is seen as the brain/pial surface. I was conservative with these as well. I have been looking on the wiki for a way to adjust the actual surface lines manually based on the actual white matter/brain surface. I think this would be most useful, but I'm not sure if it is possible. If so, how could this be done - and, if not, what possible way of trouble shooting can help deal with this white matter as pial surface issue? Best regards, - Jennifer Lynn Sarai Kriegel MS in Psychological Sciences, Cognition and Neuroscience Emphasis Functional Neuroimaging of Memory Lab, Center for Vital Longevity The University of Texas at Dallas jlk130...@utdallas.edumailto:jlk130...@utdallas.edu I am looking for a lot of men who have an infinite capacity to not know what can't be done. - Henry Ford The important thing is not to stop questioning. Curiosity has its own reason for existing. - Albert Einstein ___ 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] Skullstrip problems
Hi Paul, My apologies - what I meant was PRIOR to running skull strip, that freesurfer mistakenly made my surfaces the dura and pial, which meant removing the dura was a corrective issue. A prior member of my lab, and others whom I have asked advice on freesurfer said the same thing - the dura actually interferes with your measures of brain. From the attachment you sent, nothing vital is being removed. I wouldn't worry about re-running it. Best, Jennifer -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Paul Schauer Sent: Tuesday, June 30, 2015 7:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] Skullstrip problems Hi Jennifer, thank you for your speedy answer.:-) Unfortunately I didn't understand all of it. The problems with the skullstrip did not (!) affect any of the surfaces in this case and no grey or white matter was cut out. What I was interested in is whether any other measures might be affected (except for the dura volume which I am not interested in). Especially whether it affects any of the volume-based analysis? To put it in a nutshell: Would you rerun the skullstrip with different watershed-parameters so as to prevent the skullstrip to be overly aggressive and bite these chunks out of the dura? Or would you leave it like it is? Thanks again! Best, Paul Quoting Kriegel, Jennifer Lynn Sarai jlk130...@utdallas.edu: Hi Paul, From my understanding, that's the stuff that can interfere with your surfaces. I've run g-cut skullstrip on volumes where the surface of the pial is seen as the white matter, and the dura is seen as the cortical/pial surface. I think in terms of cortical measures, such as cortical thickness, you're better off having run the stripping. I could be wrong, but unless you're interested specifically in the dura volume as well, it's not going to affect your brain volume measure. Best regards, Jennifer Kriegel -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Paul Schauer Sent: Tuesday, June 30, 2015 7:03 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Skullstrip problems Hi all, I ran the normal recon-all -i... -s... -all on a couple of subjects and I realized that the skullstrip often seems to bite a chunk out of the meninges (see attached screenshot). Whilst the wm- and pial-surfaces seem unaffected and no grey or white matter seems to be missing I didn't bother too much. But I was asking myself whether these missing chunks did not indirectly affect these measures? Or any other measures such as the whole brain volume? Any help would be greatly appreciated! Best, Paul -- Paul Schauer, M.Sc. Psychologie Biological Psychology Neuropsychology Faculty of Psychology Human Movement Science | University of Hamburg Von-Melle-Park 11 | Room 204 | 20146 Hamburg, Germany +49 (0)40 42838 4573 ___ 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. -- Paul Schauer, M.Sc. Psychologie Biological Psychology Neuropsychology Faculty of Psychology Human Movement Science | University of Hamburg Von-Melle-Park 11 | Room 204 | 20146 Hamburg, Germany +49 (0)40 42838 4573 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Skullstrip problems
Hi Paul, From my understanding, that's the stuff that can interfere with your surfaces. I've run g-cut skullstrip on volumes where the surface of the pial is seen as the white matter, and the dura is seen as the cortical/pial surface. I think in terms of cortical measures, such as cortical thickness, you're better off having run the stripping. I could be wrong, but unless you're interested specifically in the dura volume as well, it's not going to affect your brain volume measure. Best regards, Jennifer Kriegel -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Paul Schauer Sent: Tuesday, June 30, 2015 7:03 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Skullstrip problems Hi all, I ran the normal recon-all -i... -s... -all on a couple of subjects and I realized that the skullstrip often seems to bite a chunk out of the meninges (see attached screenshot). Whilst the wm- and pial-surfaces seem unaffected and no grey or white matter seems to be missing I didn't bother too much. But I was asking myself whether these missing chunks did not indirectly affect these measures? Or any other measures such as the whole brain volume? Any help would be greatly appreciated! Best, Paul -- Paul Schauer, M.Sc. Psychologie Biological Psychology Neuropsychology Faculty of Psychology Human Movement Science | University of Hamburg Von-Melle-Park 11 | Room 204 | 20146 Hamburg, Germany +49 (0)40 42838 4573 ___ 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] sagittal slices
I used the following command to convert a sagittal slice from analyze to mgz format. The original was acquired in an anterior to posterior/right to left angle of slices. However, while it is converting to an mgz properly, it seems to be giving me a flip upside down, and reverting to transverse orientation. How do I specify for the sagittal slice? Thanks. $FREESURFER_HOME/bin/mri_convert \ $SUBJECTS_DIR/fmri35_MPRAGE_o17/fmri35_MPRAGE_o17_0001.img -it analyze --in_orientation PIR \ $SUBJECTS_DIR/fmri35_o17/mri/orig/001.mgz - Jennifer Lynn Sarai Kriegel MS in Psychological Sciences, Cognition and Neuroscience Emphasis Functional Neuroimaging of Memory Lab, Center for Vital Longevity The University of Texas at Dallas jlk130...@utdallas.edumailto:jlk130...@utdallas.edu I am looking for a lot of men who have an infinite capacity to not know what can't be done. - Henry Ford The important thing is not to stop questioning. Curiosity has its own reason for existing. - Albert Einstein ___ 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] bad magic number
Hi Jalmar, Thanks, that's very helpful because the files I am working with have been transformed more than once, and were originally par/rec files. I do not have those original files - I only have the analyze files which I was trying to convert to .nii, since the hdr file gives a different error than the bad magic number from the .nii. The transformation matrix sounds like it was the answer I was looking for but I wouldn't know where to find it, or what it should contain. I appreciate this information. Best, Jennifer -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Jalmar Teeuw Sent: Wednesday, June 10, 2015 4:10 AM To: Freesurfer support list Subject: Re: [Freesurfer] bad magic number Hi Jennifer, We had the same problem with importing scans into Freesurfer that had been converted from PAR/REC to NIFTI using nipy. The problem only affected a subset of the data. When visualising the data with Fiji the brain appeared highly skewed. Upon closer inspection of the header data of the NIFTI file we discovered that there was an extra byte somewhere between the description fields and the magic number sequence, causing the magic number to be misinterpreted by Freesurfer. The extra byte was somewhere in the transformation matrix that is located between the description field and the magic number, but it's impossible to fix unless you know what the content of the transformation matrix is supposed to be. However, when using dcm2nii, part of mricron (from what I understand a newer version of mricro), to convert our PAR/REC files to NIFTI the problem disappeared. Maybe you could try dcm2nii and see if that helps your case as well? It's available from here: http://www.mccauslandcenter.sc.edu/mricro/mricron/install.html If you are on Linux or Mac OS X you could try to run the command `head -c350 path-to-nifti-file | hexdump -Cv`, where path-to-nifti-file is the path to your NIFTI file. This command will print the first 350 bytes of the NIFTI file that contains the header (plus two extra bytes) in hexadecimal and ASCII format. I don't have an example available at the moment, but the header should end in 'ni1..' or 'n+1..' in the rightmost column. If you get 'ni1.' or 'n+1.' (only one dot at the end), you probably have the same problem as we experienced. We don't know the origin of this extra byte, but most likely it is a bug in the conversion software that is affecting only some of the scans. Regards, Jalmar On 09 Jun 2015, at 22:21, Kriegel, Jennifer Lynn Sarai jlk130...@utdallas.edu wrote: mricro -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, June 09, 2015 3:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bad magic number how was it created? On 06/09/2015 04:03 PM, Kriegel, Jennifer Lynn Sarai wrote: MRIcro opens it, and so does SPM 8. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, June 09, 2015 3:02 PM To: Freesurfer support list Subject: Re: [Freesurfer] bad magic number Hi Jennifer can MRIcro read it? Usually that means it is corrupted Bruce On Tue, 9 Jun 2015, Kriegel, Jennifer Lynn Sarai wrote: Hi, I’m getting a bad magic number error using mri_convert. I’m trying to convert a .nii file to a .mgz file. I’ve searched all over and all I can find is that you can use python in another program to delete this number, and it is related to the file extension. I’ve tried using the .nifti1 extension, as well as .nii, as I have a .img file in the folder as well, but then it doesn’t recognize the file extension. The files were converted using mricro from hdr/img MPRAGE files to correct orientation into the .nii files. I also tried using the original .hdr file to convert, and it spits out an orientation error. Any help would be appreciated. - Jennifer Lynn Sarai Kriegel MS in Psychological Sciences, Cognition and Neuroscience Emphasis Functional Neuroimaging of Memory Lab, Center for Vital Longevity The University of Texas at Dallas jlk130...@utdallas.edu I am looking for a lot of men who have an infinite capacity to not know what can't be done. - Henry Ford The important thing is not to stop questioning. Curiosity has its own reason for existing. - Albert Einstein ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Re: [Freesurfer] bad magic number
mricro -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, June 09, 2015 3:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bad magic number how was it created? On 06/09/2015 04:03 PM, Kriegel, Jennifer Lynn Sarai wrote: MRIcro opens it, and so does SPM 8. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, June 09, 2015 3:02 PM To: Freesurfer support list Subject: Re: [Freesurfer] bad magic number Hi Jennifer can MRIcro read it? Usually that means it is corrupted Bruce On Tue, 9 Jun 2015, Kriegel, Jennifer Lynn Sarai wrote: Hi, I’m getting a bad magic number error using mri_convert. I’m trying to convert a .nii file to a .mgz file. I’ve searched all over and all I can find is that you can use python in another program to delete this number, and it is related to the file extension. I’ve tried using the .nifti1 extension, as well as .nii, as I have a .img file in the folder as well, but then it doesn’t recognize the file extension. The files were converted using mricro from hdr/img MPRAGE files to correct orientation into the .nii files. I also tried using the original .hdr file to convert, and it spits out an orientation error. Any help would be appreciated. - Jennifer Lynn Sarai Kriegel MS in Psychological Sciences, Cognition and Neuroscience Emphasis Functional Neuroimaging of Memory Lab, Center for Vital Longevity The University of Texas at Dallas jlk130...@utdallas.edu I am looking for a lot of men who have an infinite capacity to not know what can't be done. - Henry Ford The important thing is not to stop questioning. Curiosity has its own reason for existing. - Albert Einstein ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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://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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] bad magic number
Hi, I'm getting a bad magic number error using mri_convert. I'm trying to convert a .nii file to a .mgz file. I've searched all over and all I can find is that you can use python in another program to delete this number, and it is related to the file extension. I've tried using the .nifti1 extension, as well as .nii, as I have a .img file in the folder as well, but then it doesn't recognize the file extension. The files were converted using mricro from hdr/img MPRAGE files to correct orientation into the .nii files. I also tried using the original .hdr file to convert, and it spits out an orientation error. Any help would be appreciated. - Jennifer Lynn Sarai Kriegel MS in Psychological Sciences, Cognition and Neuroscience Emphasis Functional Neuroimaging of Memory Lab, Center for Vital Longevity The University of Texas at Dallas jlk130...@utdallas.edumailto:jlk130...@utdallas.edu I am looking for a lot of men who have an infinite capacity to not know what can't be done. - Henry Ford The important thing is not to stop questioning. Curiosity has its own reason for existing. - Albert Einstein ___ 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] bad magic number
MRIcro opens it, and so does SPM 8. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, June 09, 2015 3:02 PM To: Freesurfer support list Subject: Re: [Freesurfer] bad magic number Hi Jennifer can MRIcro read it? Usually that means it is corrupted Bruce On Tue, 9 Jun 2015, Kriegel, Jennifer Lynn Sarai wrote: Hi, I’m getting a bad magic number error using mri_convert. I’m trying to convert a .nii file to a .mgz file. I’ve searched all over and all I can find is that you can use python in another program to delete this number, and it is related to the file extension. I’ve tried using the .nifti1 extension, as well as .nii, as I have a .img file in the folder as well, but then it doesn’t recognize the file extension. The files were converted using mricro from hdr/img MPRAGE files to correct orientation into the .nii files. I also tried using the original .hdr file to convert, and it spits out an orientation error. Any help would be appreciated. - Jennifer Lynn Sarai Kriegel MS in Psychological Sciences, Cognition and Neuroscience Emphasis Functional Neuroimaging of Memory Lab, Center for Vital Longevity The University of Texas at Dallas jlk130...@utdallas.edu I am looking for a lot of men who have an infinite capacity to not know what can't be done. - Henry Ford The important thing is not to stop questioning. Curiosity has its own reason for existing. - Albert Einstein ___ 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.
