Re: [Freesurfer] Extract mean time series from parcellated region
Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: sabin khadka sabink...@yahoo.com; Freesurfer Support List freesurfer@nmr.mgh.harvard.edu Sent: Monday, January 26, 2015 5:33 PM Subject: Re: [Freesurfer] Extract mean time series from parcellated region what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz # mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ 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 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] Extraction of T2 map statistics-per-segment
— I (think that) I am not really interested in converting into rawavg coordinate system, but just need to register my T2 maps to the segmentation maps. So, I guess that aseg+aparc.mgz will suffice in my case — Regarding the mean +- std values: Yes - the T2 maps are whole brain. could that account for the large STD? I have tried running it w/o --seg-erode.… the mean values stay similar yet, the standard-deviation increases significantly. I’ve also tried erode=2 pixels, which gave identical results to erode=1 pixel. With erode (2 pixels): # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2125567 125567.0 Left-Cerebral-White-Matter97.9045 68.8609 0. 4000. 4000. 2 7 1083310833.0 Left-Cerebellum-White-Matter 1.1878 14.7193 0. 608. 608. 3 41130433 130433.0 Right-Cerebral-White-Matter 96.1764 60.0490 0. 4000. 4000. 4 46 1155111551.0 Right-Cerebellum-White-Matter 1.2395 15.3000 0. 453. 453. With erode (1 pixel): # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2125567 125567.0 Left-Cerebral-White-Matter97.9045 68.8609 0. 4000. 4000. 2 7 1083310833.0 Left-Cerebellum-White-Matter 1.1878 14.7193 0. 608. 608. 3 41130433 130433.0 Right-Cerebral-White-Matter 96.1764 60.0490 0. 4000. 4000. 4 46 1155111551.0 Right-Cerebellum-White-Matter 1.2395 15.3000 0. 453. 453. Without erode: # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2193533 193533.0 Left-Cerebral-White-Matter99.1265 125.6069 0. 4000. 4000. 2 7 1779417794.0 Left-Cerebellum-White-Matter 7.2259 65.3060 0. 4000. 4000. 3 41197895 197895.0 Right-Cerebral-White-Matter 96.9839 115.9002 0. 4000. 4000. 4 46 1799917999.0 Right-Cerebellum-White-Matter 6.0798 88.1490 0. 4000. 4000. It’s indeed encouraging that using the erode option decreases the STD, but I’m still wondering whether there a way to validate accuracy of the values. Thanks! Noam On Jan 27, 2015, at 6:50 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: On 1/27/15 12:38 PM, Ben Eliezer, Noam wrote: Thanks Doug. I’ve made two changes to the set of commands. 1. Following your suggestion, I’ve shifted from --init-spm to --init-header and now tkregister2 shows that the registration is OK. tkregister2 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat —surf Thanks! 2. When loading the result of vol2vol command (T2_siemens_reg.mgz): mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg-in-rawavg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg into freeview the maps are rotated 90-deg in-plane and 90-deg through plane versus the segmentation maps — in short they do not match in orientation. I’ve solved this by changing from using aseg+aparc-in-rawavg.mgz to aseg+aparg.mgz mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg Question1: Is that a correct approach? not to use the rawavg coordinate system? Oh, I did not see that. Yes, that is the problem. If you want to use the rawavg coordinate system, then you'll have to create another registration file because the one that you have only goes between the T2 and the conformed 256 1mm space. Let me know if that is what you want. — Now, I re- gather statistics using: mri_segstats --seg $FSsubjDIR/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1 and get the following values: # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2125567 125567.0 Left-Cerebral-White-Matter97.9045 68.8609 0. 4000. 4000. 2 7 1083310833.0 Left-Cerebellum-White-Matter 1.1878 14.7193 0. 608. 608. 3 41130433 130433.0 Right-Cerebral-White-Matter 96.1764 60.0490 0. 4000. 4000. 4 46 1155111551.0 Right-Cerebellum-White-Matter 1.2395 15.3000 0. 453. 453. Question 2: Is there any way to verify that these values are accurate…? (I am a little worried by the large standard deviation values) Yes, I see what you mean. Is the T2 whole brain? Have you tried it without --seg-erode? Thanks again for the prompt replies, — Noam On Jan 27, 2015, at 6:02 PM, Douglas Greve
Re: [Freesurfer] Extraction of T2 map statistics-per-segment
The maps were generated by Siemens scanner, fitting a multi-spin-echo protocol. I see your point, though. The values should not range between 0 to 4000. The latter 4000 value is the background out-of-brain map value. But when looking at the T2_siemens_reg.mgz, overlaid on the aparc+aseg.mgz in freeview, the white matter (segment #2) seems well within the brain, and does not include any parts that have value = 0 or 4000. Question 1: is it possible to look at the actual set of values that are used to calculate these mean and STD result? This would probably give some hint as to the large std. Perhaps there are small number of outliers that contribute to the large variation? Question 2: (just to put my mind at rest): if both tkregister2 and freeview show show that the maps register accurately on the segmentation data, does it mean that mri_segstats masks the T2 maps correctly? I’m asking this because if the segmentation masks are off by, e.g., 90-degree, it would cause to a large number of values=4000 to be included in the mean/std values. Thanks! — Noam On Jan 27, 2015, at 7:30 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: It is finding 0s in the T2 (the range is 0-4000). I'm not sure about the 4000, but the 0s indicate that something is strange with that image. How was it created? On 1/27/15 1:22 PM, Ben Eliezer, Noam wrote: — I (think that) I am not really interested in converting into rawavg coordinate system, but just need to register my T2 maps to the segmentation maps. So, I guess that aseg+aparc.mgz will suffice in my case — Regarding the mean +- std values: Yes - the T2 maps are whole brain. could that account for the large STD? I have tried running it w/o --seg-erode.… the mean values stay similar yet, the standard-deviation increases significantly. I’ve also tried erode=2 pixels, which gave identical results to erode=1 pixel. With erode (2 pixels): # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2125567 125567.0 Left-Cerebral-White-Matter97.9045 68.8609 0. 4000. 4000. 2 7 1083310833.0 Left-Cerebellum-White-Matter 1.1878 14.7193 0. 608. 608. 3 41130433 130433.0 Right-Cerebral-White-Matter 96.1764 60.0490 0. 4000. 4000. 4 46 1155111551.0 Right-Cerebellum-White-Matter 1.2395 15.3000 0. 453. 453. With erode (1 pixel): # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2125567 125567.0 Left-Cerebral-White-Matter97.9045 68.8609 0. 4000. 4000. 2 7 1083310833.0 Left-Cerebellum-White-Matter 1.1878 14.7193 0. 608. 608. 3 41130433 130433.0 Right-Cerebral-White-Matter 96.1764 60.0490 0. 4000. 4000. 4 46 1155111551.0 Right-Cerebellum-White-Matter 1.2395 15.3000 0. 453. 453. Without erode: # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2193533 193533.0 Left-Cerebral-White-Matter99.1265 125.6069 0. 4000. 4000. 2 7 1779417794.0 Left-Cerebellum-White-Matter 7.2259 65.3060 0. 4000. 4000. 3 41197895 197895.0 Right-Cerebral-White-Matter 96.9839 115.9002 0. 4000. 4000. 4 46 1799917999.0 Right-Cerebellum-White-Matter 6.0798 88.1490 0. 4000. 4000. It’s indeed encouraging that using the erode option decreases the STD, but I’m still wondering whether there a way to validate accuracy of the values. Thanks! Noam On Jan 27, 2015, at 6:50 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: On 1/27/15 12:38 PM, Ben Eliezer, Noam wrote: Thanks Doug. I’ve made two changes to the set of commands. 1. Following your suggestion, I’ve shifted from --init-spm to --init-header and now tkregister2 shows that the registration is OK. tkregister2 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat —surf Thanks! 2. When loading the result of vol2vol command (T2_siemens_reg.mgz): mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg-in-rawavg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg into freeview the maps are rotated 90-deg in-plane and 90-deg through plane versus the segmentation maps — in short they do not match in orientation. I’ve solved this by changing from using aseg+aparc-in-rawavg.mgz to aseg+aparg.mgz mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg Question1: Is that a correct approach? not to use the rawavg coordinate system? Oh, I did not see that. Yes, that is the problem. If you
Re: [Freesurfer] retinotopy in subject volumetric space
Hello, When I try your recommended code, I am able to get the data back into volumetric space, but one hemisphere's cortex is significantly thinner than the other. If I do mri_surf2vol separately on each hemisphere, I don't have this problem. It seems to occur only if I try merging the two files. I assume that this is because I am using the volume that I am merging to as a template instead of inputting the template directly. Do you have any ideas how to solve this problem? Thanks for your help, Ben On Wed, Dec 24, 2014 at 2:57 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: I don't think we have a tool to display the color wheel in a volume. FreeView might be able to do it. For the color wheel in tksurfer, you are looking at the angle file (one for eccen and one for polar), so you would map them. You can run mri_surf2vol something like mri_surf2vol --surfval lh.angle.nii.gz --identity yoursubject --hemi lh --template path/orig.mgz --fillribbon --o vol.angle.mgz mri_surf2vol --surfval rh.angle.nii.gz --identity yoursubject --hemi rh --fillribbon --merge vol.angle.mgz --o vol.angle.mgz doug On 12/18/14 1:24 PM, Benjamin Zimmerman wrote: I mean the individual's anatomical volumetric space. On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: What do you mean by the individual's volumetric space? The anatomical space or the functional space? On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote: Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to what the retinotopy analysis outputs. To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an individual's volumetric space. I can load these as overlays to the inflated surface using tksurfer subject hemisphere inflated. Then I can configure the overlay to use a color wheel color scale and display as complex to see the retinotopic mapping. I'm not sure how I would go about using mri_surf2vol to recreate this map in volumetric space. Should I just use real.nii.gz and imag.nii.gz as surfval? Where is the registration file outputted in a retinotopy analysis? Thank you for any more help that you can provide, Ben On Mon, Dec 15, 2014 at 3:26 PM, dgw dgwake...@gmail.com mailto:dgwake...@gmail.com wrote: Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has an excellent individual retinotopy analysis that allows me to see phase data on the inflated surface of the brain. Is there a way to view the results of the retinotopy analysis in the subject's original volumetric space rather than on the subject's surface space? Thank you for any help, Ben ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: 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 -- 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 ___ Freesurfer mailing
[Freesurfer] eTIV correction and registration in common space
Hi list,please, I have two questions:a) subcortical volume correction in cross-sectional studies could be done by using total GM as covariate instead of eTIV?b) relatively to group subcortical analysis in cross-sectional studies, the anatomical images should be necessarily transformed in common space or is possible to perform the analysis in native space?The registration in common space should minimize issues due to different head size. The computation on native space could bias the results considering the different head sizes among subjects?Thanks, Stefano ___ 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] Converting dicom images to nifti
p.s. sorry, I missed the multiframe part. I guess dcmunpack and mri_convert won't work, but maybe decompressing and using something else afterwards will do the trick? On Tue, 27 Jan 2015, Douglas Greve wrote: If you run it with --help there will be lots of documentation and examples. It will not be able to convert the multiframe dicom files though On 1/27/15 12:24 PM, pradeep mahato wrote: Please tell how to use dcmunpack. Any help converting dicom to nii. On Jan 27, 2015 9:03 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Pradeep, I don't think that we can convert that either. Sorry. doug On 1/27/15 7:18 AM, pradeep mahato wrote: Hi experts, I am trying to convert dicom images namely 00A0,00A1,00A2 [ No file extension ] etc. These are generated by Philips machine. I used dcm2nii, it does not give correct result. It gives warning : this software will only convert the first slice of this multislice lossless compressed JPEG . In one thread I read that dicom images from Philips scanner are oriented differently. I tried to use dcmunpack method, but I am not able to save the converted image. I used dcmunpack -src srcDirc. Please share the correct procedure. In one of the subjects I have very less number of images:30. Is it necessary to have more dicom images to have a better brain mri image . If yes, what should be the optimal number of images Thanking You Pradeep Kumar Mahato ___ 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Extract mean time series from parcellated region
Works fine. thanks for the help Doug. Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: sabin khadka sabink...@yahoo.com; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, January 27, 2015 12:33 PM Subject: Re: [Freesurfer] Extract mean time series from parcellated region That label2vol command maps the aseg into the epi space to create test1 so it will only have 1 frame. The epi never comes into play there except as a geometry template. If you want to extract a time course from the epi, then map it to the anatomical space with that vol2vol command using the epi as the --mov, then run mri_segstats. That label2vol command is not necessary. doug On 1/27/15 12:13 PM, sabin khadka wrote: Hi doug. I now see the problem. When I run mri_info the test1.nii.gz and test2.nii.gz both have only 1 frame. But when I run # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz EPI.nii.gz is 4D image with 210 frames. How can I get test1.nii.gz and test2.nii.gz in 4D format? Should be something basic but I could not figure out how. I appreciate your help!! Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: sabin khadka sabink...@yahoo.com; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, January 27, 2015 10:31 AM Subject: Re: [Freesurfer] Extract mean time series from parcellated region It all looks correct. How many frames does test2.nii.gz have? Try running mri_info test2.nii.gz to see On 1/27/15 9:05 AM, sabin khadka wrote: Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: sabin khadka sabink...@yahoo.com; Freesurfer Support List freesurfer@nmr.mgh.harvard.edu Sent: Monday, January 26, 2015 5:33 PM Subject: Re: [Freesurfer] Extract mean time series from parcellated region what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz # mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ 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 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] Extraction of T2 map statistics-per-segment
It is finding 0s in the T2 (the range is 0-4000). I'm not sure about the 4000, but the 0s indicate that something is strange with that image. How was it created? On 1/27/15 1:22 PM, Ben Eliezer, Noam wrote: — I (think that) I am not really interested in converting into rawavg coordinate system, but just need to register my T2 maps to the segmentation maps. So, I guess that aseg+aparc.mgz will suffice in my case — Regarding the mean +- std values: Yes - the T2 maps are whole brain. could that account for the large STD? I have tried running it w/o --seg-erode.… the mean values stay similar yet, the standard-deviation increases significantly. I’ve also tried erode=2 pixels, which gave identical results to erode=1 pixel. With erode (2 pixels): # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2125567 125567.0 Left-Cerebral-White-Matter 97.9045 68.8609 0. 4000. 4000. 2 7 1083310833.0 Left-Cerebellum-White-Matter 1.1878 14.7193 0. 608. 608. 3 41130433 130433.0 Right-Cerebral-White-Matter 96.1764 60.0490 0. 4000. 4000. 4 46 1155111551.0 Right-Cerebellum-White-Matter 1.2395 15.3000 0. 453. 453. With erode (1 pixel): # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2125567 125567.0 Left-Cerebral-White-Matter 97.9045 68.8609 0. 4000. 4000. 2 7 1083310833.0 Left-Cerebellum-White-Matter 1.1878 14.7193 0. 608. 608. 3 41130433 130433.0 Right-Cerebral-White-Matter 96.1764 60.0490 0. 4000. 4000. 4 46 1155111551.0 Right-Cerebellum-White-Matter 1.2395 15.3000 0. 453. 453. Without erode: # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2193533 193533.0 Left-Cerebral-White-Matter 99.1265 125.6069 0. 4000. 4000. 2 7 1779417794.0 Left-Cerebellum-White-Matter 7.2259 65.3060 0. 4000. 4000. 3 41197895 197895.0 Right-Cerebral-White-Matter 96.9839 115.9002 0. 4000. 4000. 4 46 1799917999.0 Right-Cerebellum-White-Matter 6.0798 88.1490 0. 4000. 4000. It’s indeed encouraging that using the erode option decreases the STD, but I’m still wondering whether there a way to validate accuracy of the values. Thanks! Noam On Jan 27, 2015, at 6:50 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 1/27/15 12:38 PM, Ben Eliezer, Noam wrote: Thanks Doug. I’ve made two changes to the set of commands. *1.* Following your suggestion, I’ve shifted from --init-spm to --init-header and now tkregister2 shows that the registration is OK. tkregister2 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat —surf Thanks! *2.* When loading the result of vol2vol command (T2_siemens_reg.mgz): mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg-in-rawavg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg into freeview the maps are rotated 90-deg in-plane and 90-deg through plane versus the segmentation maps — in short they do not match in orientation. I’ve solved this by changing from using aseg+aparc-in-rawavg.mgz to aseg+aparg.mgz mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg _Question1:_ Is that a correct approach? not to use the rawavg coordinate system? Oh, I did not see that. Yes, that is the problem. If you want to use the rawavg coordinate system, then you'll have to create another registration file because the one that you have only goes between the T2 and the conformed 256 1mm space. Let me know if that is what you want. — Now, I re- gather statistics using: mri_segstats --seg $FSsubjDIR/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1 and get the following values: # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2125567 125567.0 Left-Cerebral-White-Matter 97.904568.8609 0. 4000. 4000. 2 7 1083310833.0 Left-Cerebellum-White-Matter 1.187814.7193 0. 608. 608. 3 41130433 130433.0 Right-Cerebral-White-Matter 96.176460.0490 0. 4000. 4000. 4 46 1155111551.0 Right-Cerebellum-White-Matter 1.239515.3000 0. 453. 453. _Question 2:_ Is there any way to verify that these values are accurate…? (I am a little worried by the large standard deviation values) Yes, I see what you mean. Is the T2 whole brain? Have you tried it
Re: [Freesurfer] Converting dicom images to nifti
have you tried dcmdjpeg or dcmdjpls to uncompress them, then used some other unpacker/converter (mri_convert etc...) cheers Bruce On Tue, 27 Jan 2015, pradeep mahato wrote: Please tell how to use dcmunpack. Any help converting dicom to nii. On Jan 27, 2015 9:03 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Pradeep, I don't think that we can convert that either. Sorry. doug On 1/27/15 7:18 AM, pradeep mahato wrote: Hi experts, I am trying to convert dicom images namely 00A0,00A1,00A2 [ No file extension ] etc. These are generated by Philips machine. I used dcm2nii, it does not give correct result. It gives warning : this software will only convert the first slice of this multislice lossless compressed JPEG . In one thread I read that dicom images from Philips scanner are oriented differently. I tried to use dcmunpack method, but I am not able to save the converted image. I used dcmunpack -src srcDirc. Please share the correct procedure. In one of the subjects I have very less number of images:30. Is it necessary to have more dicom images to have a better brain mri image . If yes, what should be the optimal number of images Thanking You Pradeep Kumar Mahato ___ 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 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] retinotopy in subject volumetric space
Ugh, that's weird, I don't know what's going on with that. I'll have to dig into it more. On 1/27/15 1:26 PM, Benjamin Zimmerman wrote: Hello, When I try your recommended code, I am able to get the data back into volumetric space, but one hemisphere's cortex is significantly thinner than the other. If I do mri_surf2vol separately on each hemisphere, I don't have this problem. It seems to occur only if I try merging the two files. I assume that this is because I am using the volume that I am merging to as a template instead of inputting the template directly. Do you have any ideas how to solve this problem? Thanks for your help, Ben On Wed, Dec 24, 2014 at 2:57 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I don't think we have a tool to display the color wheel in a volume. FreeView might be able to do it. For the color wheel in tksurfer, you are looking at the angle file (one for eccen and one for polar), so you would map them. You can run mri_surf2vol something like mri_surf2vol --surfval lh.angle.nii.gz --identity yoursubject --hemi lh --template path/orig.mgz --fillribbon --o vol.angle.mgz mri_surf2vol --surfval rh.angle.nii.gz --identity yoursubject --hemi rh --fillribbon --merge vol.angle.mgz --o vol.angle.mgz doug On 12/18/14 1:24 PM, Benjamin Zimmerman wrote: I mean the individual's anatomical volumetric space. On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: What do you mean by the individual's volumetric space? The anatomical space or the functional space? On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote: Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to what the retinotopy analysis outputs. To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an individual's volumetric space. I can load these as overlays to the inflated surface using tksurfer subject hemisphere inflated. Then I can configure the overlay to use a color wheel color scale and display as complex to see the retinotopic mapping. I'm not sure how I would go about using mri_surf2vol to recreate this map in volumetric space. Should I just use real.nii.gz and imag.nii.gz as surfval? Where is the registration file outputted in a retinotopy analysis? Thank you for any more help that you can provide, Ben On Mon, Dec 15, 2014 at 3:26 PM, dgw dgwake...@gmail.com mailto:dgwake...@gmail.com mailto:dgwake...@gmail.com mailto:dgwake...@gmail.com wrote: Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has an excellent individual retinotopy analysis that allows me to see phase data on the inflated surface of the brain. Is there a way to view the results of the retinotopy analysis in the subject's original volumetric space rather than on the subject's surface space? Thank you for any help, Ben ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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
[Freesurfer] MNI to RAS?
Hi, Is there an easy way to convert MNI coordinates to Freesurfer RAS coordinate space? Thanks! Cat ___ 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] eTIV correction and registration in common space
Hi Steano a) You could do this but then you are testing a somewhat different hypothesis - that the change in a specific structure is more than the overall change in gray matter. Thus for example, widespread atrophy would be regressed out. If that's what you are interested in, then this approach is fine. b) Our analysis is always in individual subject space. You can transform to a common space using mri_vol2vol if you want. cheers Bruce On Tue, 27 Jan 2015, std...@virgilio.it wrote: Hi list, please, I have two questions: a) subcortical volume correction in cross-sectional studies could be done by using total GM as covariate instead of eTIV? b) relatively to group subcortical analysis in cross-sectional studies, the anatomical images should be necessarily transformed in common space or is possible to perform the analysis in native space? The registration in common space should minimize issues due to different head size. The computation on native space could bias the results considering the different head sizes among subjects? Thanks, Stefano ___ 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] Extraction of T2 map statistics-per-segment
On 1/27/15 1:56 PM, Ben Eliezer, Noam wrote:
The maps were generated by Siemens scanner, fitting a multi-spin-echo
protocol.
I see your point, though. The values should not range between 0 to
4000. The latter 4000 value is the background out-of-brain map value.
But when looking at the T2_siemens_reg.mgz, overlaid on the
aparc+aseg.mgz in freeview, the white matter (segment #2) seems well
within the brain, and does not include any parts that have value = 0
or 4000.
_Question 1_: is it possible to look at the actual set of values that
are used to calculate these mean and STD result?
This would probably give some hint as to the large std. Perhaps there
are small number of outliers that contribute to the large variation?
You can use matlab, something like
t2 = MRIread('T2_siemsn_reg.mgz');
seg = MRIread('aparc+aseg.mgz');
ind = find(seg.vol == 17); % left hippo
t2hip = t2.vol(ind);
See $FREESURFER_HOME/FreeSurferColorLUT.txt for a list of segmentation
numbers
_Question 2_: (just to put my mind at rest): if both tkregister2 and
freeview show show that the maps register accurately on the
segmentation data, does it mean that mri_segstats masks the T2 maps
correctly?
I’m asking this because if the segmentation masks are off by, e.g.,
90-degree, it would cause to a large number of values=4000 to be
included in the mean/std values.
It should. You can also try
tkmedit -f t2file.mgz -seg aparc+aseg.mgz
Thanks!
— Noam
On Jan 27, 2015, at 7:30 PM, Douglas Greve gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
It is finding 0s in the T2 (the range is 0-4000). I'm not sure about
the 4000, but the 0s indicate that something is strange with that
image. How was it created?
On 1/27/15 1:22 PM, Ben Eliezer, Noam wrote:
— I (think that) I am not really interested in converting into
rawavg coordinate system, but just need to register my T2 maps to
the segmentation maps.
So, I guess that aseg+aparc.mgz will suffice in my case
— Regarding the mean +- std values:
Yes - the T2 maps are whole brain. could that account for the large STD?
I have tried running it w/o --seg-erode.… the mean values stay
similar yet, the standard-deviation increases significantly.
I’ve also tried erode=2 pixels, which gave identical results to
erode=1 pixel.
With erode (2 pixels):
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev
Min Max Range
1 2125567 125567.0 Left-Cerebral-White-Matter
97.904568.8609 0. 4000. 4000.
2 7 1083310833.0 Left-Cerebellum-White-Matter
1.187814.7193 0. 608. 608.
3 41130433 130433.0 Right-Cerebral-White-Matter
96.176460.0490 0. 4000. 4000.
4 46 1155111551.0 Right-Cerebellum-White-Matter
1.239515.3000 0. 453. 453.
With erode (1 pixel):
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev
Min Max Range
1 2125567 125567.0 Left-Cerebral-White-Matter
97.904568.8609 0. 4000. 4000.
2 7 1083310833.0 Left-Cerebellum-White-Matter
1.187814.7193 0. 608. 608.
3 41130433 130433.0 Right-Cerebral-White-Matter
96.176460.0490 0. 4000. 4000.
4 46 1155111551.0 Right-Cerebellum-White-Matter
1.239515.3000 0. 453. 453.
Without erode:
# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev
Min Max Range
1 2193533 193533.0 Left-Cerebral-White-Matter
99.1265 125.6069 0. 4000. 4000.
2 7 1779417794.0 Left-Cerebellum-White-Matter
7.225965.3060 0. 4000. 4000.
3 41197895 197895.0 Right-Cerebral-White-Matter
96.9839 115.9002 0. 4000. 4000.
4 46 1799917999.0 Right-Cerebellum-White-Matter
6.079888.1490 0. 4000. 4000.
It’s indeed encouraging that using the erode option decreases the
STD, but I’m still wondering whether there a way to validate
accuracy of the values.
Thanks!
Noam
On Jan 27, 2015, at 6:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
On 1/27/15 12:38 PM, Ben Eliezer, Noam wrote:
Thanks Doug.
I’ve made two changes to the set of commands.
*1.* Following your suggestion, I’ve shifted from --init-spm to
--init-header and now tkregister2 shows that the registration is OK.
tkregister2 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat —surf
Thanks!
*2.* When loading the result of vol2vol command (T2_siemens_reg.mgz):
mri_vol2vol --mov T2_siemens.mgz --targ
subj01/mri/aparc+aseg-in-rawavg.mgz --interp nearest --o
T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg
into freeview the maps are rotated 90-deg in-plane and 90-deg
through plane versus the segmentation maps — in short they do not
match in orientation.
I’ve
Re: [Freesurfer] longitudinal pipeline
HI Song, are you talking about the longitudinal tractography? If you have longitudinal data, then yes, we recommend the use of longitudinal processing both for the structural and for the tractography. That's what they have been developed for. Best, Martin On Jan 26, 2015, at 5:50 PM, Inkyung Song song...@nyspi.columbia.edu wrote: Hi Freesurfer Experts, Is the longitudinal pipeline still recommended for the DTI data analysis if structural changes occur at different time points (e.g., pre and post-treatment)? Or is it better to use the standard pipeline? Are other options available? Thanks so much! Song ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Dr. Martin Reuter 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 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] lme_mass_RgGrow
Hi FS experts, Two questions about the lme_mass_RgGrow command for spatiotemporal models: 1. If you're estimating a longitudinal mixed effects model with fixed effects of time (linear) and group, as well as a random effect for time, will this command segment the brain into homogeneous regions such that voxels within a homogeneous region tend to exhibit the same degree of change over time? 2. Is there any reason why it would be problematic to apply this command to source-localized EEG data (as opposed to fMRI data)? Thanks, Jordan ___ 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] Converting dicom images to nifti
Hi experts, I am trying to convert dicom images namely 00A0,00A1,00A2 [ No file extension ] etc. These are generated by Philips machine. I used dcm2nii, it does not give correct result. It gives warning : this software will only convert the first slice of this multislice lossless compressed JPEG . In one thread I read that dicom images from Philips scanner are oriented differently. I tried to use dcmunpack method, but I am not able to save the converted image. I used dcmunpack -src srcDirc. Please share the correct procedure. In one of the subjects I have very less number of images:30. Is it necessary to have more dicom images to have a better brain mri image . If yes, what should be the optimal number of images Thanking You Pradeep Kumar Mahato ___ 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] Extraction of T2 map statistics-per-segment
First off, I would use --init-header instead of --init-spm. Probably won't make a difference, but it is safer in this case. Second, look at the registration in tkregister (bbregister prints out the command line, you can just cut and paste). doug ps. Please remember to post the list instead of directly to us. thanks! On 1/27/15 11:23 AM, Ben Eliezer, Noam wrote: Hi Doug — My apologies for the confusion. Please ignore the commands set below. There is only one set of commands that I tried. It’s: mri_convert -it siemens_dicom -ot mgz SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm T2_siemens.mgz bbregister --s subj01 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat --init-spm --t2 mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg mri_segstats --seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1 But as I wrote below — loading the registered T2 map T2_siemens_reg.mgz into Freeview shows that it’s incorrectly registered on the segmentation maps. Thanks and sorry for the confusion, — Noam On Jan 27, 2015, at 5:07 PM, Ben Eliezer, Noam noam.ben-elie...@nyumc.org mailto:noam.ben-elie...@nyumc.org wrote: Hi Doug — Thank you for the prompt reply! I have indeed tried using bbregister (and consult the -- help) but I am probably not using it correctly. I’ve tried two set of commands: mri_convert -it siemens_dicom -ot mgz SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm T2_siemens.mgz bbregister --s subj01--mov T2_siemens.mgz --reg T2_siemens_regMat.dat --init-spm --t2 mri_segstats —seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1 or, mri_convert -it siemens_dicom -ot mgz SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm T2_siemens.mgz mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg mri_segstats --seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1 Both set of commands age the same statistics values, yet, in both cases the registration seemed wrong, when running: tkregister2 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat —surf so I am not sure if the values I get are ok…. Also, when loading the registered T2 maps (T2_siemens_reg.mgz) into Freeview they did not coincide with my aseg+aparc.mgz or aseg+aparc-in-rawavg.mgz Any help would be highly appreciated! Best! Noam On 1/27/15 2:11 AM, Ben Eliezer, Noam wrote: Hello --- I'm trying to extract quantitative T2 values for different brain segments. I've converted my T2 set of DICOMs to .mgz format using mri_convert and loaded them into freeview. mri_convert -it siemens_dicom -ot mgz T2_maps_Dir/slice_1_T2_map.dcm T2_in_mgz.mgz After loading T2_in_mgz.mgz to Freeview the T2 maps seem to coincide very well with the segmentation maps (aseg+aparc-in-rawavg.mgz). My questions are: 1. Should I have applied some pre-registration operation on the T2 maps before loading them into freeview, or does the fact that they coincide with the segmentation maps mean that I don't need to apply any registration? Since they are in the same session, they will be pretty close in registration, it just depends on how much the subject moved between the two acquisitions. As a matter of course, I would run a registration on them (bbregister with --init-header). This subject may not have moved much but it is no guarantee that others won't move more. 2. How can I extract mean T2 values for different segments? (not the usual volume-per-segment) Use mri_segstats. Run with --help to get examples doug Much obliged! --- Noam -- Noam Ben-Eliezer, PhD Adjunct Assistant Professor of Radiology Center for Biomedical-Imaging New-York University Medical School noam.ben-elie...@nyumc.org http://nyumc.org/ mailto:noam.ben-elie...@nyumc.org ___ 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] Extraction of T2 map statistics-per-segment
On 1/27/15 2:11 AM, Ben Eliezer, Noam wrote: Hello --- I'm trying to extract quantitative T2 values for different brain segments. I've converted my T2 set of DICOMs to .mgz format using mri_convert and loaded them into freeview. mri_convert -it siemens_dicom -ot mgz T2_maps_Dir/slice_1_T2_map.dcm T2_in_mgz.mgz After loading T2_in_mgz.mgz to Freeview the T2 maps seem to coincide very well with the segmentation maps (aseg+aparc-in-rawavg.mgz). My questions are: 1. Should I have applied some pre-registration operation on the T2 maps before loading them into freeview, or does the fact that they coincide with the segmentation maps mean that I don't need to apply any registration? Since they are in the same session, they will be pretty close in registration, it just depends on how much the subject moved between the two acquisitions. As a matter of course, I would run a registration on them (bbregister with --init-header). This subject may not have moved much but it is no guarantee that others won't move more. 2. How can I extract mean T2 values for different segments? (not the usual volume-per-segment) Use mri_segstats. Run with --help to get examples doug Much obliged! --- Noam -- Noam Ben-Eliezer, PhD Adjunct Assistant Professor of Radiology Center for Biomedical-Imaging New-York University Medical School noam.ben-elie...@nyumc.org mailto:noam.ben-elie...@nyumc.org ___ 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 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] Extract mean time series from parcellated region
It all looks correct. How many frames does test2.nii.gz have? Try running mri_info test2.nii.gz to see On 1/27/15 9:05 AM, sabin khadka wrote: Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka *From:* Douglas Greve gr...@nmr.mgh.harvard.edu *To:* sabin khadka sabink...@yahoo.com; Freesurfer Support List freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, January 26, 2015 5:33 PM *Subject:* Re: [Freesurfer] Extract mean time series from parcellated region what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz # mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 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] Converting dicom images to nifti
Hi Pradeep, I don't think that we can convert that either. Sorry. doug On 1/27/15 7:18 AM, pradeep mahato wrote: Hi experts, I am trying to convert dicom images namely 00A0,00A1,00A2 [ No file extension ] etc. These are generated by Philips machine. I used dcm2nii, it does not give correct result. It gives warning : this software will only convert the first slice of this multislice lossless compressed JPEG . In one thread I read that dicom images from Philips scanner are oriented differently. I tried to use dcmunpack method, but I am not able to save the converted image. I used dcmunpack -src srcDirc. Please share the correct procedure. In one of the subjects I have very less number of images:30. Is it necessary to have more dicom images to have a better brain mri image . If yes, what should be the optimal number of images Thanking You Pradeep Kumar Mahato ___ 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 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] Converting dicom images to nifti
If you run it with --help there will be lots of documentation and examples. It will not be able to convert the multiframe dicom files though On 1/27/15 12:24 PM, pradeep mahato wrote: Please tell how to use dcmunpack. Any help converting dicom to nii. On Jan 27, 2015 9:03 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Pradeep, I don't think that we can convert that either. Sorry. doug On 1/27/15 7:18 AM, pradeep mahato wrote: Hi experts, I am trying to convert dicom images namely 00A0,00A1,00A2 [ No file extension ] etc. These are generated by Philips machine. I used dcm2nii, it does not give correct result. It gives warning : this software will only convert the first slice of this multislice lossless compressed JPEG . In one thread I read that dicom images from Philips scanner are oriented differently. I tried to use dcmunpack method, but I am not able to save the converted image. I used dcmunpack -src srcDirc. Please share the correct procedure. In one of the subjects I have very less number of images:30. Is it necessary to have more dicom images to have a better brain mri image . If yes, what should be the optimal number of images Thanking You Pradeep Kumar Mahato ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 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] Extract mean time series from parcellated region
That label2vol command maps the aseg into the epi space to create test1 so it will only have 1 frame. The epi never comes into play there except as a geometry template. If you want to extract a time course from the epi, then map it to the anatomical space with that vol2vol command using the epi as the --mov, then run mri_segstats. That label2vol command is not necessary. doug On 1/27/15 12:13 PM, sabin khadka wrote: Hi doug. I now see the problem. When I run mri_info the test1.nii.gz and test2.nii.gz both have only 1 frame. But when I run # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz EPI.nii.gz is 4D image with 210 frames. How can I get test1.nii.gz and test2.nii.gz in 4D format? Should be something basic but I could not figure out how. I appreciate your help!! Cheers, Sabin Khadka *From:* Douglas Greve gr...@nmr.mgh.harvard.edu *To:* sabin khadka sabink...@yahoo.com; Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Sent:* Tuesday, January 27, 2015 10:31 AM *Subject:* Re: [Freesurfer] Extract mean time series from parcellated region It all looks correct. How many frames does test2.nii.gz have? Try running mri_info test2.nii.gz to see On 1/27/15 9:05 AM, sabin khadka wrote: Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka *From:* Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* sabin khadka sabink...@yahoo.com mailto:sabink...@yahoo.com; Freesurfer Support List freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, January 26, 2015 5:33 PM *Subject:* Re: [Freesurfer] Extract mean time series from parcellated region what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz # mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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 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] Extraction of T2 map statistics-per-segment
Thanks Doug. I’ve made two changes to the set of commands. 1. Following your suggestion, I’ve shifted from --init-spm to --init-header and now tkregister2 shows that the registration is OK. tkregister2 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat —surf Thanks! 2. When loading the result of vol2vol command (T2_siemens_reg.mgz): mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg-in-rawavg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg into freeview the maps are rotated 90-deg in-plane and 90-deg through plane versus the segmentation maps — in short they do not match in orientation. I’ve solved this by changing from using aseg+aparc-in-rawavg.mgz to aseg+aparg.mgz mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg Question1: Is that a correct approach? not to use the rawavg coordinate system? — Now, I re- gather statistics using: mri_segstats --seg $FSsubjDIR/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1 and get the following values: # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2125567 125567.0 Left-Cerebral-White-Matter97.9045 68.8609 0. 4000. 4000. 2 7 1083310833.0 Left-Cerebellum-White-Matter 1.1878 14.7193 0. 608. 608. 3 41130433 130433.0 Right-Cerebral-White-Matter 96.1764 60.0490 0. 4000. 4000. 4 46 1155111551.0 Right-Cerebellum-White-Matter 1.2395 15.3000 0. 453. 453. Question 2: Is there any way to verify that these values are accurate…? (I am a little worried by the large standard deviation values) Thanks again for the prompt replies, — Noam On Jan 27, 2015, at 6:02 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: First off, I would use --init-header instead of --init-spm. Probably won't make a difference, but it is safer in this case. Second, look at the registration in tkregister (bbregister prints out the command line, you can just cut and paste). doug ps. Please remember to post the list instead of directly to us. thanks! On 1/27/15 11:23 AM, Ben Eliezer, Noam wrote: Hi Doug — My apologies for the confusion. Please ignore the commands set below. There is only one set of commands that I tried. It’s: mri_convert -it siemens_dicom -ot mgz SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm T2_siemens.mgz bbregister --s subj01 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat --init-spm --t2 mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg mri_segstats --seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1 But as I wrote below — loading the registered T2 map T2_siemens_reg.mgz into Freeview shows that it’s incorrectly registered on the segmentation maps. Thanks and sorry for the confusion, — Noam On Jan 27, 2015, at 5:07 PM, Ben Eliezer, Noam noam.ben-elie...@nyumc.orgmailto:noam.ben-elie...@nyumc.org wrote: Hi Doug — Thank you for the prompt reply! I have indeed tried using bbregister (and consult the -- help) but I am probably not using it correctly. I’ve tried two set of commands: mri_convert -it siemens_dicom -ot mgz SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm T2_siemens.mgz bbregister --s subj01--mov T2_siemens.mgz --reg T2_siemens_regMat.dat --init-spm --t2 mri_segstats —seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1 or, mri_convert -it siemens_dicom -ot mgz SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm T2_siemens.mgz mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg mri_segstats --seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1 Both set of commands age the same statistics values, yet, in both cases the registration seemed wrong, when running: tkregister2 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat —surf so I am not sure if the values I get are ok…. Also, when loading the registered T2 maps (T2_siemens_reg.mgz) into Freeview they did not coincide with my aseg+aparc.mgz or aseg+aparc-in-rawavg.mgz Any help would be highly appreciated! Best! Noam On 1/27/15 2:11 AM, Ben Eliezer, Noam wrote:
Re: [Freesurfer] Extract mean time series from parcellated region
Hi doug. I now see the problem. When I run mri_info the test1.nii.gz and test2.nii.gz both have only 1 frame. But when I run# mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz# mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gzEPI.nii.gz is 4D image with 210 frames. How can I get test1.nii.gz and test2.nii.gz in 4D format? Should be something basic but I could not figure out how. I appreciate your help!! Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: sabin khadka sabink...@yahoo.com; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, January 27, 2015 10:31 AM Subject: Re: [Freesurfer] Extract mean time series from parcellated region It all looks correct. How many frames does test2.nii.gz have? Try running mri_info test2.nii.gz to see On 1/27/15 9:05 AM, sabin khadka wrote: Hi Doug- The command doesn't error out but it just give me one value. I was assuming the following command would give me value in time series x mean value in text file. Am I following correct strategy/commands? Cheers, Sabin Khadka From: Douglas Greve gr...@nmr.mgh.harvard.edu To: sabin khadka sabink...@yahoo.com; Freesurfer Support List freesurfer@nmr.mgh.harvard.edu Sent: Monday, January 26, 2015 5:33 PM Subject: Re: [Freesurfer] Extract mean time series from parcellated region what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz # mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ 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 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] Converting dicom images to nifti
Please tell how to use dcmunpack. Any help converting dicom to nii. On Jan 27, 2015 9:03 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Pradeep, I don't think that we can convert that either. Sorry. doug On 1/27/15 7:18 AM, pradeep mahato wrote: Hi experts, I am trying to convert dicom images namely 00A0,00A1,00A2 [ No file extension ] etc. These are generated by Philips machine. I used dcm2nii, it does not give correct result. It gives warning : this software will only convert the first slice of this multislice lossless compressed JPEG . In one thread I read that dicom images from Philips scanner are oriented differently. I tried to use dcmunpack method, but I am not able to save the converted image. I used dcmunpack -src srcDirc. Please share the correct procedure. In one of the subjects I have very less number of images:30. Is it necessary to have more dicom images to have a better brain mri image . If yes, what should be the optimal number of images Thanking You Pradeep Kumar Mahato ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 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] Extraction of T2 map statistics-per-segment
On 1/27/15 12:38 PM, Ben Eliezer, Noam wrote: Thanks Doug. I’ve made two changes to the set of commands. *1.* Following your suggestion, I’ve shifted from --init-spm to --init-header and now tkregister2 shows that the registration is OK. tkregister2 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat —surf Thanks! *2.* When loading the result of vol2vol command (T2_siemens_reg.mgz): mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg-in-rawavg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg into freeview the maps are rotated 90-deg in-plane and 90-deg through plane versus the segmentation maps — in short they do not match in orientation. I’ve solved this by changing from using aseg+aparc-in-rawavg.mgz to aseg+aparg.mgz mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg _Question1:_ Is that a correct approach? not to use the rawavg coordinate system? Oh, I did not see that. Yes, that is the problem. If you want to use the rawavg coordinate system, then you'll have to create another registration file because the one that you have only goes between the T2 and the conformed 256 1mm space. Let me know if that is what you want. — Now, I re- gather statistics using: mri_segstats --seg $FSsubjDIR/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1 and get the following values: # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 2125567 125567.0 Left-Cerebral-White-Matter 97.9045 68.8609 0. 4000. 4000. 2 7 1083310833.0 Left-Cerebellum-White-Matter 1.1878 14.7193 0. 608. 608. 3 41130433 130433.0 Right-Cerebral-White-Matter 96.1764 60.0490 0. 4000. 4000. 4 46 1155111551.0 Right-Cerebellum-White-Matter 1.2395 15.3000 0. 453. 453. _Question 2:_ Is there any way to verify that these values are accurate…? (I am a little worried by the large standard deviation values) Yes, I see what you mean. Is the T2 whole brain? Have you tried it without --seg-erode? Thanks again for the prompt replies, — Noam On Jan 27, 2015, at 6:02 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: First off, I would use --init-header instead of --init-spm. Probably won't make a difference, but it is safer in this case. Second, look at the registration in tkregister (bbregister prints out the command line, you can just cut and paste). doug ps. Please remember to post the list instead of directly to us. thanks! On 1/27/15 11:23 AM, Ben Eliezer, Noam wrote: Hi Doug — My apologies for the confusion. Please ignore the commands set below. There is only one set of commands that I tried. It’s: mri_convert -it siemens_dicom -ot mgz SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm T2_siemens.mgz bbregister --s subj01 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat --init-spm --t2 mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg mri_segstats --seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1 But as I wrote below — loading the registered T2 map T2_siemens_reg.mgz into Freeview shows that it’s incorrectly registered on the segmentation maps. Thanks and sorry for the confusion, — Noam On Jan 27, 2015, at 5:07 PM, Ben Eliezer, Noam noam.ben-elie...@nyumc.org mailto:noam.ben-elie...@nyumc.org wrote: Hi Doug — Thank you for the prompt reply! I have indeed tried using bbregister (and consult the -- help) but I am probably not using it correctly. I’ve tried two set of commands: mri_convert -it siemens_dicom -ot mgz SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm T2_siemens.mgz bbregister --s subj01--mov T2_siemens.mgz --reg T2_siemens_regMat.dat --init-spm --t2 mri_segstats —seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1 or, mri_convert -it siemens_dicom -ot mgz SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm T2_siemens.mgz mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz --interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg mri_segstats --seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1 Both set of commands age the same statistics values, yet, in both cases
