Re: [Freesurfer] Cortical gray matter surface area
Thanks Doug, Just to double check I understand you correctly, where the output says # Measure Cortex, WhiteSurfArea, White Surface Total Area this is now the surface area of the pial surface even though it is labeled White? Cheers, Will On Sat, Sep 13, 2014 at 3:27 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You can run something like cd $SUBJECTS_DIR/subject mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab subject lh pial The Measure Cortex fields in the output stats/lh.aparc.pial.stats will be measures of the pial surface as will the SurfArea, MeanCurv, GausCurv, FoldInd, and CurvInd fields for each ROI (thickness and number of vertices will stay the same) doug On 09/11/2014 07:29 PM, will brown wrote: Sure. We'd like to know how to find the surface area of the cortical grey matter from the pial surface. So specifically, what is the surface area of the pial/grey matter boundary of the cortex for each hemisphere? We're using Freesurfer v5.3 on Centos 6. Thanks, Will Brown On Fri, Sep 12, 2014 at 9:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: sorry, this thread has gotten too deep. Can someone summarize the question? On Thu, 11 Sep 2014, _andre...@sapo.pt mailto:andre...@sapo.pt wrote: Ok. Then, I'm not sure if everything is correct with the command lines since I use 5.0. Any thought on this Freesurfer team? Thanks, Andreia Citando will brown willbrown1...@gmail.com mailto:willbrown1...@gmail.com: Thanks again, for the record, I'm using freesurfer version 5.3.0 on Centos 6. On 9/09/2014 11:00 PM, _andre...@sapo.pt mailto:andre...@sapo.pt wrote: Hi Will, Just to clarify, what version of FS are you using? I think it might not be 5.0 and I don't know if everything aplies if we are using different versions. 1) Yes, it is only based on the pial surface (and these command lines are for the aparc, DK altas). The second set provides the surface area for each hemisphere without including, for example, the pial surface that you see in the hippocampus which is not accurate and one should not care about. In the end, the second set gives you the sum of the areas in aparc, thus, you can just make a sum of that parcellation if you want. I just realized that. 2) No. In the new stats file, the value that you want is at the bottom: # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd And when running aparcstats2table that's the value you should get in the table. I think that # Measure Cortex, WhiteSurfArea, White Surface Total Area may be including more stuff since it is bigger. If what you want is only the total hemisphere surface area you only need to run the second set of commands. If you want the area of each DK altas parcellation then run the first set and then simply add them to get total hemisphere surface area. Someone from Freesurfer staff will correct me if I'm wrong. (Please) I'm Ccing Doug since he was replying to your previous emails. Let's wait for their feedback. Andreia Citando will brown willbrown1...@gmail.com mailto:willbrown1...@gmail.com: Thanks Andreia, this does appear to have worked. Please forgive my ignorance but I do just want to double check two things; 1) The first commands you have given provide the stats for the two hemispheres of the cerebral cortex only based on the pial surface, whereas the second set of commands provide the pial boundary stats for the whole brain rather than just cortex? 2) The surface area value that I am looking for (grey matter surface area at the grey/pial boundary) is listed in the new stats table next to: # Measure Cortex, WhiteSurfArea, White Surface Total Area, ? Thanks again, Will On Tue, Sep 9, 2014 at 5:36 PM, will brown willbrown1...@gmail.com
[Freesurfer] fsfast: using an empirically derived HRF with mkanalysis-sess
hi freesurfers, i would like to use an empirically derived HRF with mkanalysis-sess. i have derived the HRF i want [via an FIR model], but it's not obvious how i can use my custom HRF with mkanalysis-sess. one option, it seems, is to feed in my own regressors with the -taskreg flag and then not supply the model with any other regressors of interest. i'd just convolve stick regressors that have the appropriate timing with my own HRF. but this would only work if selxavg3-sess does NOT convolve task regressors with the HRF. so two questions: 1. is the -taskreg flag the best way to do this? is there another, better way? 2. does selxavg3-sess convolve task regressors with the HRF? thanks, alex ___ 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] fsfast: using an empirically derived HRF with mkanalysis-sess
and one point of clarification: i only care about beta weights for each condition of interest, so i don't care that -taskreg would only run an F-test for significance maps and wouldn't give me t maps for each regressor of interest. thanks again, alex On Sun, Sep 14, 2014 at 1:55 PM, Alex Kell alexk...@mit.edu wrote: hi freesurfers, i would like to use an empirically derived HRF with mkanalysis-sess. i have derived the HRF i want [via an FIR model], but it's not obvious how i can use my custom HRF with mkanalysis-sess. one option, it seems, is to feed in my own regressors with the -taskreg flag and then not supply the model with any other regressors of interest. i'd just convolve stick regressors that have the appropriate timing with my own HRF. but this would only work if selxavg3-sess does NOT convolve task regressors with the HRF. so two questions: 1. is the -taskreg flag the best way to do this? is there another, better way? 2. does selxavg3-sess convolve task regressors with the HRF? thanks, alex ___ 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] fsfast: using an empirically derived HRF with mkanalysis-sess
On 9/14/14 1:55 PM, Alex Kell wrote: hi freesurfers, i would like to use an empirically derived HRF with mkanalysis-sess. i have derived the HRF i want [via an FIR model], but it's not obvious how i can use my custom HRF with mkanalysis-sess. one option, it seems, is to feed in my own regressors with the -taskreg flag and then not supply the model with any other regressors of interest. i'd just convolve stick regressors that have the appropriate timing with my own HRF. but this would only work if selxavg3-sess does NOT convolve task regressors with the HRF. so two questions: 1. is the -taskreg flag the best way to do this? is there another, better way? Yea, I think so. I think i added some capability to spec custom HRFs, but it was a long time ago and might not have make the conversion to version 5 2. does selxavg3-sess convolve task regressors with the HRF? No, it does not, so you're good to go. thanks, alex ___ 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] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
yep, you can use it for anything. doug On 9/14/14 12:52 PM, Salil Soman wrote: Dear Doug, Thank you again for this email. Do you think it is possible to use this method for ASL images as well? If so, how would you change the options? Best wishes, Salil Soman, MD, MS On Sat, May 25, 2013 at 11:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 5/25/13 1:39 PM, Salil Soman wrote: Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat That is right, but add --t2 (since it is t2 weighted). *2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff). *3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats The input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add --seg-erode 1 to erode the segmentations by a voxel. This helps to prevent partial voluming. doug Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table? I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be? Best wishes, Sal On Sat, May 25, 2013 at 10:06 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman wrote: Dear Dr. Greve, Is it possible to register a nonstructural MR sequences (e.g. an ADC map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using the segmentation from the aseg (or aparc+aseg) file to output a mean ADC value for each anatomic area segmented? Thank you for your time and consideration. Best wishes, Sal Salil Soman, MD, MS 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. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ 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] sMRI using Freesurfer 5.1 followed by DTI using Freesufer 5.3
Hi, Could you please let me know if it's okay to use subjects analyzed using Freesurfer 5.1 (os x 10.6) for DTI analysis using Freesurfer 5.3 (os x 10.8)? Thanks. ___ 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] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Thank you Doug. I am having trouble with extracting statistics using this method. I am able to use bbregister to get a transformation that registers the PD image of the ASL to the T1. I then used this transformation matrix to register the CBF map for the ASL study into the T1.mgz space. Checking the images, the registration looked reasonable. However, when I try to extract the values from the registered image using the vois from aparc+aseg.mgz, and the FreeSurferColorLUT I get all 0 values. *The command I ran is:* mri_segstats --seg $SUBJECTS_DIR/SUBJECT_ID/mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i SUBJECT_ID_CBF_reg.nii.gz --sum SUBJECT_ID_ASL.stats --seg-erode 1 *where SUBJECT_ID_CBF_reg.nii.gz was generated by running:* mri_vol2vol --mov SUBJECT_ID_CBF.nii.gz --targ T1.mgz --interp nearest --o SUBJECT_ID_CBF_reg.nii.gz --reg SUBJECT_ID.dat --no-save-reg (and this was run with T1.mgz and SUBJECT_ID_CBF.nii.gz in the same folder). *for which SUBJECT_ID.dat was generated by running the code:* bbregister --s SUBJECT_ID --mov SUBJECT_ID_ASL_PD.nii.gz --reg SUBJECT_ID.dat --t1 --init-fsl Thank you for your consideration of this question. Best wishes, Salil Soman, MD, MS On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: yep, you can use it for anything. doug On 9/14/14 12:52 PM, Salil Soman wrote: Dear Doug, Thank you again for this email. Do you think it is possible to use this method for ASL images as well? If so, how would you change the options? Best wishes, Salil Soman, MD, MS On Sat, May 25, 2013 at 11:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: On 5/25/13 1:39 PM, Salil Soman wrote: Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat That is right, but add --t2 (since it is t2 weighted). *2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff). *3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats The input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add --seg-erode 1 to erode the segmentations by a voxel. This helps to prevent partial voluming. doug Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table? I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be? Best wishes, Sal On Sat, May 25, 2013 at 10:06 AM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman wrote: Dear Dr. Greve, Is it possible to register a nonstructural MR sequences (e.g. an ADC map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using the segmentation from the aseg (or aparc+aseg) file to output a mean ADC value for each anatomic area segmented? Thank you for your time and consideration. Best wishes, Sal Salil Soman, MD, MS 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. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological
