Re: [Freesurfer] mri_vol2surf --projopt
Allright, if the option --interp nearest is used the output is as given in a previous post (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35148.html). After applying --interp trilin the output is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --interp trilin --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map.gm.mgz reading wm volume fraction from /.../map.wm.mgz reading csf volume fraction from /.../map.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --interp trilin --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault If the option --interp is dissmissed completely the output is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map.gm.mgz reading wm volume fraction from /.../map.wm.mgz reading csf volume fraction from /.../map.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault Voxel size of the epi and the map data from mri_compute_volume_fractions is 1.5 x 1.5 x 2 mm^3 and of the t1 image is 1 x 1 x 1 mm^3. On Mon, 14 Apr 2014 12:24:37 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you send your commandline with --interp as well as the terminal output? On 04/14/2014 06:54 AM, Joerg Pfannmoeller wrote: Well, there is no difference between trilin or nearest. mri_vol2surf displays segfault regardless which option I use (trilin or nearest). On Thu, 10 Apr 2014 11:30:38 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I don't understand what the question is. If you need to interpolate, then use --interp trilinear doug On 04/10/2014 04:36 AM, Joerg Pfannmoeller wrote: Allright! The only point I would like to emphasize is: Regardless if option trilin or nearest is used I need to interpolate the functional data to the structural image of the subject. This might be due to a feature of the function build_sample_array in the mri_vol2surf source code. In this function there are some constant values (din = 1.0, dout = 0.1, nsamples = 10), which might be the reason why I need to interpolate the functional data to the structural image. Currently I can not investigate the code any further. Do you have enough experience with the source code to clarify this question? On Wed, 09 Apr 2014 09:31:57 -0400 Douglas Greve gr...@nmr.mgh.harvard.edu wrote: You can use --projfrac (which can perform an interpolation with --interp trilinear) On 4/9/14 2:44 AM, Joerg Pfannmoeller wrote: Sorry for this question, but now I am confused. Do you mean that I should not use projopt and just use the interpolation? If so why should I not use projfrac? On Tue, 08 Apr 2014 15:02:36 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to do without it for now and just do the interpolation On 04/08/2014 03:32 AM, Joerg Pfannmoeller wrote: Well, I need to use that option. In this case I will just interpolate to the 1 mm grid and proceed this way. On Mon, 07 Apr 2014 12:14:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Sorry, I don't understand. You mean it still segfaults without --projopt or that you have to use projopt? On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote: Unfortunately that is no option for me. On Fri, 04 Apr 2014 15:33:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Don't use --projopt and it won't segfault On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote: The command is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex The output is the follwoing: srcvol =
[Freesurfer] Mask and Label
Hi, I have two unrelated questions: 1) I have three mask files: mask1.nii.gz, mask2.nii.gz, mask3.nii.gz. The masks might be overlapping. I want to make a new mask file in which vertices that are 1 in mask1 or mask2 or mask3 get the value of 1, and vertices that are 0 in all three masks get the value of 0. How can I do that? 2) I have a text file containing a list of vertices in a column format. How can I convert it to a label file? Thanks, Reza ___ 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] FS volume discrepancies
I have several issues concerning automated volumes calculation. When you look at the aseg.stat for hippocampal volume (in mm3) it gives different value compared to hippocampal subfields volume calculation (which comes in voxels but there is stated that 1 voxel is 0.5mm3). How is it possible? I presume that anatomical definition and subfield incorporation is the same. Next - if you look at the whole hippocampal formation volume in hippocampal subfield calculations it is way lower compared to the summation of the CA1- CA4 + dentate gyrus = hippocampal formation. What could be explanation of this? Petr___ 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] Mask and Label
1. mri_or mask1.nii.gz, mask2.nii.gz, mask3.nii.gz mask.total.mgz 2. Put it in a text file and add 4 more columns of zeros so that each row has the vertex index followed by 4 zeroes (with spaces between them) cheers Bruce On Tue, 15 Apr 2014, Reza Rajimehr wrote: Hi, I have two unrelated questions: 1) I have three mask files: mask1.nii.gz, mask2.nii.gz, mask3.nii.gz. The masks might be overlapping. I want to make a new mask file in which vertices that are 1 in mask1 or mask2 or mask3 get the value of 1, and vertices that are 0 in all three masks get the value of 0. How can I do that? 2) I have a text file containing a list of vertices in a column format. How can I convert it to a label file? Thanks, Reza ___ 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] FS volume discrepancies
From Eugenio: Dear Petr, at this point, the hippocampal subfield module is - to some extent - independent from the whole hippocampal segmentation. The values you will obtain from adding the subfield volumes together will be around 15% lower than the volumes from aseg.stat, but they will still be very highly correlated. Kind regards, On Tue, 15 Apr 2014, zach.p...@post.cz wrote: I have several issues concerning automated volumes calculation. When you look at the aseg.stat for hippocampal volume (in mm3) it gives different value compared to hippocampal subfields volume calculation (which comes in voxels but there is stated that 1 voxel is 0.5mm3). How is it possible? I presume that anatomical definition and subfield incorporation is the same. Next - if you look at the whole hippocampal formation volume in hippocampal subfield calculations it is way lower compared to the summation of the CA1-CA4 + dentate gyrus = hippocampal formation. What could be explanation of this? Petr ___ 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] FS volume discrepancies
Thanks for reply. But adding subfield volumes together leads to too high number compared to overall hippocampus volume. Like 9500 mm3 compared to 2.1 mm3. Petr -- Původní zpráva -- Od: Bruce Fischl fis...@nmr.mgh.harvard.edu Komu: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Datum: 15. 4. 2014 14:35:13 Předmět: Re: [Freesurfer] FS volume discrepancies From Eugenio: Dear Petr, at this point, the hippocampal subfield module is - to some extent - independent from the whole hippocampal segmentation. The values you will obtain from adding the subfield volumes together will be around 15% lower than the volumes from aseg.stat, but they will still be very highly correlated. Kind regards, On Tue, 15 Apr 2014, zach.p...@post.cz wrote: I have several issues concerning automated volumes calculation. When you look at the aseg.stat for hippocampal volume (in mm3) it gives different value compared to hippocampal subfields volume calculation (which comes in voxels but there is stated that 1 voxel is 0.5mm3). How is it possible? I presume that anatomical definition and subfield incorporation is the same. Next - if you look at the whole hippocampal formation volume in hippocampal subfield calculations it is way lower compared to the summation of the CA1-CA4 + dentate gyrus = hippocampal formation. What could be explanation of this? Petr ___ 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] FS volume discrepancies
Dear Petr, the volumes from the subfields are in voxels. Since the voxels are 0.5mm isotropic, their volumes is (1/8) cubic millimeters. Therefore, you need to divide the volumes by 8 to convert to mm3. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: zach petr zach.p...@post.cz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, April 15, 2014 4:05:43 PM Subject: Re: [Freesurfer] FS volume discrepancies Thanks for reply. But adding subfield volumes together leads to too high number compared to overall hippocampus volume. Like 9500 mm3 compared to 2.1 mm3. Petr -- Původní zpráva -- Od: Bruce Fischl fis...@nmr.mgh.harvard.edu Komu: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Datum: 15. 4. 2014 14:35:13 Předmět: Re: [Freesurfer] FS volume discrepancies From Eugenio: Dear Petr, at this point, the hippocampal subfield module is - to some extent - independent from the whole hippocampal segmentation. The values you will obtain from adding the subfield volumes together will be around 15% lower than the volumes from aseg.stat, but they will still be very highly correlated. Kind regards, On Tue, 15 Apr 2014, zach.p...@post.cz wrote: I have several issues concerning automated volumes calculation. When you look at the aseg.stat for hippocampal volume (in mm3) it gives different value compared to hippocampal subfields volume calculation (which comes in voxels but there is stated that 1 voxel is 0.5mm3). How is it possible? I presume that anatomical definition and subfield incorporation is the same. Next - if you look at the whole hippocampal formation volume in hippocampal subfield calculations it is way lower compared to the summation of the CA1-CA4 + dentate gyrus = hippocampal formation. What could be explanation of this? Petr ___ 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
Re: [Freesurfer] FS volume discrepancies
Great! OK. Now I understand. Thanks for reply. Petr -- Původní zpráva -- Od: Eugenio Iglesias e.igles...@bcbl.eu Komu: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Datum: 15. 4. 2014 16:18:59 Předmět: Re: [Freesurfer] FS volume discrepancies Dear Petr, the volumes from the subfields are in voxels. Since the voxels are 0.5mm isotropic, their volumes is (1/8) cubic millimeters. Therefore, you need to divide the volumes by 8 to convert to mm3. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: zach petr zach.p...@post.cz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, April 15, 2014 4:05:43 PM Subject: Re: [Freesurfer] FS volume discrepancies Thanks for reply. But adding subfield volumes together leads to too high number compared to overall hippocampus volume. Like 9500 mm3 compared to 2.1 mm3. Petr -- Původní zpráva -- Od: Bruce Fischl fis...@nmr.mgh.harvard.edu Komu: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Datum: 15. 4. 2014 14:35:13 Předmět: Re: [Freesurfer] FS volume discrepancies From Eugenio: Dear Petr, at this point, the hippocampal subfield module is - to some extent - independent from the whole hippocampal segmentation. The values you will obtain from adding the subfield volumes together will be around 15% lower than the volumes from aseg.stat, but they will still be very highly correlated. Kind regards, On Tue, 15 Apr 2014, zach.p...@post.cz wrote: I have several issues concerning automated volumes calculation. When you look at the aseg.stat for hippocampal volume (in mm3) it gives different value compared to hippocampal subfields volume calculation (which comes in voxels but there is stated that 1 voxel is 0.5mm3). How is it possible? I presume that anatomical definition and subfield incorporation is the same. Next - if you look at the whole hippocampal formation volume in hippocampal subfield calculations it is way lower compared to the summation of the CA1-CA4 + dentate gyrus = hippocampal formation. What could be explanation of this? Petr ___ 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;___ 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] 1 PostDoc + 2 PhD positions in Computational Cognitive NeuroImaging; University of Birmingham, UK
*2 PhD and 1 PostDoc positions in Computational Cognitive Neuroimaging; University of Birmingham, UK* In our natural dynamic environment the senses are constantly bombarded with many different signals. How does the human brain integrate information from multiple senses during perception? To study the neural mechanisms of multisensory integration and learning, we combine psychophysics, functional imaging (fMRI, EEG/MEG interleaved TMS-fMRI) and models of Bayesian Inference and learning. The Computational Cognitive Neuroimaging Group (Prof Uta Noppeney) is seeking 1 enthusiastic PostDoc and 2 PhD candidates. Applicants should have astrong quantitative background and a degree in neuroscience, psychology, computer science, physics, medicine or related areas. Prior experience in functional imaging, MatLab, data analysis and/or machine learning would be an advantage. The lab is part of the Computational Neuroscience and Cognitive Robotics Centre and the Department of Psychology of the University of Birmingham, UK. The centre provides an excellent multidisciplinary and collaborative research environment combining expertise in cognitive neuroimaging, psychophysics and computational neuroscience. The psychology department was rated 3rd in the UK research assessment exercise. Applications will be considered until the positions are filled. Starting dates are flexible. For further information, please contact u.noppe...@bham.ac.uk mailto:u.noppe...@bham.ac.uk and see http://www.birmingham.ac.uk/research/activity/cncr/index.aspx http://www.birmingham.ac.uk/schools/psychology/index.aspx http://www.birmingham.ac.uk/schools/psychology/index.aspx http://www.birmingham.ac.uk/schools/psychology/people/profile.aspx?ReferenceId=29516 http://www.birmingham.ac.uk/schools/psychology/people/profile.aspx?ReferenceId=29516 For application to the PostDoc positions, please send applications to http://www.jobs.ac.uk/job/AIM528/research-fellow/ For application to the PhD positions, please send application including CV, statement of research interests, and the names and full contact details of two referees to:u.noppe...@bham.ac.uk mailto:u.noppe...@bham.ac.uk ___ 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] mri_vol2surf --projopt
Don't use --projopt On 04/15/2014 02:21 AM, Joerg Pfannmoeller wrote: Allright, if the option --interp nearest is used the output is as given in a previous post (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35148.html). After applying --interp trilin the output is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --interp trilin --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map.gm.mgz reading wm volume fraction from /.../map.wm.mgz reading csf volume fraction from /.../map.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --interp trilin --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault If the option --interp is dissmissed completely the output is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map.gm.mgz reading wm volume fraction from /.../map.wm.mgz reading csf volume fraction from /.../map.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f001.dof6.dat --projopt /.../map --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault Voxel size of the epi and the map data from mri_compute_volume_fractions is 1.5 x 1.5 x 2 mm^3 and of the t1 image is 1 x 1 x 1 mm^3. On Mon, 14 Apr 2014 12:24:37 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you send your commandline with --interp as well as the terminal output? On 04/14/2014 06:54 AM, Joerg Pfannmoeller wrote: Well, there is no difference between trilin or nearest. mri_vol2surf displays segfault regardless which option I use (trilin or nearest). On Thu, 10 Apr 2014 11:30:38 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I don't understand what the question is. If you need to interpolate, then use --interp trilinear doug On 04/10/2014 04:36 AM, Joerg Pfannmoeller wrote: Allright! The only point I would like to emphasize is: Regardless if option trilin or nearest is used I need to interpolate the functional data to the structural image of the subject. This might be due to a feature of the function build_sample_array in the mri_vol2surf source code. In this function there are some constant values (din = 1.0, dout = 0.1, nsamples = 10), which might be the reason why I need to interpolate the functional data to the structural image. Currently I can not investigate the code any further. Do you have enough experience with the source code to clarify this question? On Wed, 09 Apr 2014 09:31:57 -0400 Douglas Greve gr...@nmr.mgh.harvard.edu wrote: You can use --projfrac (which can perform an interpolation with --interp trilinear) On 4/9/14 2:44 AM, Joerg Pfannmoeller wrote: Sorry for this question, but now I am confused. Do you mean that I should not use projopt and just use the interpolation? If so why should I not use projfrac? On Tue, 08 Apr 2014 15:02:36 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to do without it for now and just do the interpolation On 04/08/2014 03:32 AM, Joerg Pfannmoeller wrote: Well, I need to use that option. In this case I will just interpolate to the 1 mm grid and proceed this way. On Mon, 07 Apr 2014 12:14:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Sorry, I don't understand. You mean it still segfaults without --projopt or that you have to use projopt? On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote: Unfortunately that is no option for me. On Fri, 04 Apr 2014 15:33:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Don't use --projopt and it won't segfault On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote: The command is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape
Re: [Freesurfer] Mask and Label
On 04/15/2014 02:26 AM, Reza Rajimehr wrote: Hi, I have two unrelated questions: 1) I have three mask files: mask1.nii.gz, mask2.nii.gz, mask3.nii.gz. The masks might be overlapping. I want to make a new mask file in which vertices that are 1 in mask1 or mask2 or mask3 get the value of 1, and vertices that are 0 in all three masks get the value of 0. How can I do that? Try something like fscalc mask1.nii.gz or mask2.nii.gz or mask3.nii.gz -o newmask.nii.gz 2) I have a text file containing a list of vertices in a column format. How can I convert it to a label file? Look in one of the label files for guidance. The first two lines look like #!ascii label , from subject vox2ras=TkReg 138440 You can copy the first line. The 2nd line is the number of points in the label. The remainder are the list of 0-based vertices, like 0 -13.187 -94.944 10.964 0.00 1 -13.603 -94.969 10.844 0.00 2 -14.359 -94.940 10.636 0.00 3 -14.817 -94.894 10.617 0.00 4 -13.233 -94.957 10.522 0.00 For a surface-based label, you can just fill in the first column and set the other 4 numbers to 0 doug Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Thickness values to a common space
Hi all, Related question to this. I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject subject dir area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. For some reason I am not able to post questions to freesurfer support list by myself. Thanks for the help. -Sabin On Friday, April 11, 2014 3:18 PM, Jonathan Holt whats...@umich.edu wrote: I’m trying to find a way to extract thickness values at each vertex for a given subject, and as a part of that process I need to ensure that each subject has been mapped to a common area, such that their vertices have a direct correspondence, but I’m not entirely sure how to go about it. I’ve started with mris_preproc but the output is an mgh, which I’m not sure is useful for my endeavor. ___ 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] Thickness values to a common space
what is your command line? The one below is not a valid command line. On 04/15/2014 11:23 AM, sabin khadka wrote: Hi all, Related question to this. I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject subject dir area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. For some reason I am not able to post questions to freesurfer support list by myself. Thanks for the help. -Sabin On Friday, April 11, 2014 3:18 PM, Jonathan Holt whats...@umich.edu wrote: I’m trying to find a way to extract thickness values at each vertex for a given subject, and as a part of that process I need to ensure that each subject has been mapped to a common area, such that their vertices have a direct correspondence, but I’m not entirely sure how to go about it. I’ve started with mris_preproc but the output is an mgh, which I’m not sure is useful for my endeavor. ___ 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 -- 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
Re: [Freesurfer] Thickness values to a common space
Hi Doug, Thanks for the reply. Those are the two steps I followed to extract vertexwise surface area, thickness and pial_lgi values Step 1: mri_surf2surf --hemi ?h --srcsubject SUB001 [thickness, area or pial_lgi] --src_type curv --trgsubject fsaverage --trgsurfval SUB001-area --trg_type curv Step 2: mris_convert -c SUB001-area ?h.white SUB001-area.asc Can you direct me on how to get vertex wise thickness, surface area and pial_lgi values for a subject and extract in a ascii file. And also, if I want to convert ascii file with thickness values to freesurfer format, how would I do it? Thanks, Sabin On Tuesday, April 15, 2014 11:29 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is your command line? The one below is not a valid command line. On 04/15/2014 11:23 AM, sabin khadka wrote: Hi all, Related question to this. I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject subject dir area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. For some reason I am not able to post questions to freesurfer support list by myself. Thanks for the help. -Sabin On Friday, April 11, 2014 3:18 PM, Jonathan Holt whats...@umich.edu wrote: I’m trying to find a way to extract thickness values at each vertex for a given subject, and as a part of that process I need to ensure that each subject has been mapped to a common area, such that their vertices have a direct correspondence, but I’m not entirely sure how to go about it. I’ve started with mris_preproc but the output is an mgh, which I’m not sure is useful for my endeavor. ___ 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 -- 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 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] Thickness values to a common space
Can you send the exact command line you are using (no wildcards or substitutions) and the terminal output that you get? On 04/15/2014 11:52 AM, sabin khadka wrote: Hi Doug, Thanks for the reply. Those are the two steps I followed to extract vertexwise surface area, thickness and pial_lgi values Step 1: mri_surf2surf --hemi ?h --srcsubject SUB001 [thickness, area or pial_lgi] --src_type curv --trgsubject fsaverage --trgsurfval SUB001-area --trg_type curv Step 2: mris_convert -c SUB001-area ?h.white SUB001-area.asc Can you direct me on how to get vertex wise thickness, surface area and pial_lgi values for a subject and extract in a ascii file. And also, if I want to convert ascii file with thickness values to freesurfer format, how would I do it? Thanks, Sabin On Tuesday, April 15, 2014 11:29 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is your command line? The one below is not a valid command line. On 04/15/2014 11:23 AM, sabin khadka wrote: Hi all, Related question to this. I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject subject dir area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. For some reason I am not able to post questions to freesurfer support list by myself. Thanks for the help. -Sabin On Friday, April 11, 2014 3:18 PM, Jonathan Holt whats...@umich.edu mailto:whats...@umich.edu wrote: I’m trying to find a way to extract thickness values at each vertex for a given subject, and as a part of that process I need to ensure that each subject has been mapped to a common area, such that their vertices have a direct correspondence, but I’m not entirely sure how to go about it. I’ve started with mris_preproc but the output is an mgh, which I’m not sure is useful for my endeavor. ___ 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 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 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 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
Re: [Freesurfer] hippocampal subfield segmentation
To whom it may concern, I'm writing in regard to the thread below about using the sum of the hippocampal subfield volumes (excluding the hippocampal fissure). I'm finding that they are moderate-highly correlated with the hippocampal volumes from ASEG (~.75-.85). Do you have a sense of which of these measures would be more reliable than the other? Thanks so much for your help!! Best, Mike On Wed, 2013-06-05 at 10:54 +0200, Claudia Dacquino wrote: Thank you for your response. Would you suggest a reference I can refer to? 2013/6/4 Juan Eugenio Iglesias iglesias at nmr.mgh.harvard.edu I would probably leave out the fissure, but not the fimbria... Cheers, /Eugenio On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote: Hi guys! I have a dataset including hippocampal subfields obtained through the -hippo-subfields flag. I want to have a measure of total hippo volume and I'm not sure which structures should I include in the sum. I was thinking to exclude fimbria and fissure and sum the others. Am I right? Or should I simply sum all the structures? Any help is more than welcome Cheers, Fabrizio ___ Freesurfer mailing list Freesurfer at nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias at nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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. -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias at nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. --- Mike Strupp-Levitsky, BA Data Manager Image Analyst Molecular Imaging Neuropathology Division Columbia University, Department of Psychiatry New York State Psychiatric Institute, Suite 3920 (W): 646-774-7531 (C): 607-227-8811 Email: ms4...@columbia.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] FreeSurfer Course in Copenhagen
FreeSurfer Course Copenhagen 2014 We are pleased to announce a European FreeSurfer Course that will be held from August 11th to 13th 2014 in Copenhagen, Denmark. The course will be organized by the Neurobiology Research Unit, Copenhagen University Hospital and the Department for Computer Science of the University of Copenhagen in cooperation with the Laboratory for Computational Neuroimaging of the Athinoula A. Martinos Center for Biomedical Imaging. The course will be a three-day course for beginners and experienced users of FreeSurfer and the lectures will be held by FreeSurfer developers from the Laboratory for Computational Neuroimaging of the Athinoula A. Martinos Center for Biomedical Imaging. For further information and to register for this course, please visit: https://fscph2014.nru.dk Allison ___ 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] hippocampal subfield segmentation
Hi Mike, We have found that the volumes obtained by summing the subfield volumes discriminates a bit better between controls and AD subjects than the standard FS hippocampal volumes. Hope this helps, Koen On Tue, Apr 15, 2014 at 7:11 PM, Mike Strupp-Levitsky ms4...@columbia.edu wrote: To whom it may concern, I'm writing in regard to the thread below about using the sum of the hippocampal subfield volumes (excluding the hippocampal fissure). I'm finding that they are moderate-highly correlated with the hippocampal volumes from ASEG (~.75-.85). Do you have a sense of which of these measures would be more reliable than the other? Thanks so much for your help!! Best, Mike On Wed, 2013-06-05 at 10:54 +0200, Claudia Dacquino wrote: Thank you for your response. Would you suggest a reference I can refer to? 2013/6/4 Juan Eugenio Iglesias iglesias at nmr.mgh.harvard.edu I would probably leave out the fissure, but not the fimbria... Cheers, /Eugenio On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote: Hi guys! I have a dataset including hippocampal subfields obtained through the -hippo-subfields flag. I want to have a measure of total hippo volume and I'm not sure which structures should I include in the sum. I was thinking to exclude fimbria and fissure and sum the others. Am I right? Or should I simply sum all the structures? Any help is more than welcome Cheers, Fabrizio ___ Freesurfer mailing list Freesurfer at nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias at nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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. -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias at nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. --- Mike Strupp-Levitsky, BA Data Manager Image Analyst Molecular Imaging Neuropathology Division Columbia University, Department of Psychiatry New York State Psychiatric Institute, Suite 3920 (W): 646-774-7531 (C): 607-227-8811 Email: ms4...@columbia.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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Surface-based label to a mask
Hi, Is there an easy way to convert a surface-based label to a mask without going to Matlab? Thanks, Reza ___ 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] Surface-based label to a mask
use mri_label2label with --outmask On 04/15/2014 06:02 PM, Reza Rajimehr wrote: Hi, Is there an easy way to convert a surface-based label to a mask without going to Matlab? Thanks, Reza ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
Hi, Doug. Thanks a lot! The command would look like this: mri_glmfit-sim --glmdir lh.thickness.Sch.glmdir --sim mc-z 1 2 teste --sim-sign abs --overwrite --cache 1.3 abs It takes only a few seconds to run. I have a few questions about how to run it: 1) How the single entry for each subject look like in the FSGD file? 2) How to define the voxel/vertex-wise used to define clusters (after —sim, -log10( p)), and the voxel-wise threshold for the —cache option? What is the difference between them? Thanks again, Pedro Rosa. On Monday, April 14, 2014 at 3:29 PM, Douglas N Greve wrote: On 04/14/2014 10:35 AM, Pedro Rosa wrote: Dear Doug and Jorge, I tried what you suggested and I think it work, although I have some concerns. I am working with a longitudinal study with two time-points for all subjects, three categorical variables (group, substance abuse / dependence and gender) and three continuous variables (interval between scans, age and medication intake). I generated a contrast with intercept + 7 betas for the LME, ran it without any problem and saved the sig.mgh using fs_write_fstats(F_lhstats,mri,’sig.mgh’,’sig’). For the mri_glmfit I entered the same output from mri_surf2surf I used for the LME (smoothed at 10mm), but I did not know how exactly to enter the categorical and continuous variables, or which contrast to use. I would do it as a paired-test (see the wiki). You may have to re-run mris_preproc with the --paired-diff flag, then smooth by 10mm. Use this as the input to mri_glmfit. Set up the FSGD with the categorical and continuous variables (note that the FSGD file will have only a single entry per subject). Create your contrasts and run mri_glmfit. Overwrite the sig.mgh with the one from LME. Then run mri_glmfit-sim with the --cache option (not permutation) I don't know what your contrast of interest is, so I can't help you there. In the end, it does not matter because you are overwriting the sig map anyway. You just need a contrast as a place holder. doug The commmand was: mri_glmfit —y pval.mgh —sim perm 1 0.05 sch I just tested creating a matrix with 24 columns (Nclasses*(Nvariables+1) as suggested for DODS). Afterwards I ran the mri_glmfit-sim (mri_glmfit-sim --glmdir Sch-glmdir --sim mc-full 5 2 teste --sim-sign abs, and it finished apparently without errors. I attached the logs for both mri_glmfit and mri_glmfit-sim. That said, I have the following questions: 1) What does the FWHM procedure does? 2) How should I decide which contrast to test if the mri_glmfit does not consider the longitudinal design? 3) Will the mri_glmfit-sim consider only the FMHM output from mri_glmfit and sig.mgh from the LME, or also other outputs from the mri_glmfit? 4) Does the FWHM rely only on the images, and not on variables and contrasts? Thank you very much! Pedro Rosa. On Monday, March 31, 2014 at 10:53 PM, Pedro Rosa wrote: Thanks, Doug! Should I run the mri_preproc and and smooth the output using mri_surf2surf with, let’s say, 10mm, and than run the LME normally in MatLab? Would this be problematic with a different smoothing procedure in mri_glmfit? How will mri_glmfit deal with the longitudinal design? Does this matter, or the FWHM would only be estimated on a average image of all time-points for all subjects? Regards, Pedro Rosa. On Sunday, March 30, 2014 at 3:51 PM, Douglas Greve wrote: I think I would just run mri_glmfit on your data to get the proper directly structure and estimate of FWHM, then copy the sig file from the mixed fx analysis into the glmfit folder for one of the contrasts. Then run mri_glmfit-sim. doug On 3/29/14 10:29 AM, Pedro Rosa wrote: Dear Doug and Jorge, Thank you very much for your help. I found another message in the list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html) in which you suggested a way of using MC in mri_glmfit-sim by creating “fake files”, which would not be read by the script. In this case, only the simulation would be run, and not the full statistics. The command would be something like this: - mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign abs I created a “fake” mri_glmfit.log, fwhm.dat and mask.mgh files as suggested by the older post. This would be fine, I believe, if only sig.mgh is read by the script. However, I get this message after running the command: [server:Long-T0-T2-Posproc/Vertex/Sch] pedrogomesrosa% mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste --sim-sign abs if: Expression Syntax. Is it possible to do what I am trying to do? Does the residual
