[Freesurfer] Thank you
Hi everyone, I would just say you thank you for the help you give to Freesurfer users. I use Freesurfer for my school project and I ended yesterday. I didn't know anything about Linux before and before segmentation software of cortical surface. I don't think I would did an so great job without your help. Again, Thank you! And Good Luck !!! VP___ 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] GIFTI file
Hi, I saw in the documentation that since the version 5.2.0 of Freesurferw ecan open and write .gii file. I have a surface in .gii and I would like open it on FS. The fact is that, I didn't find a way to do that in the documentation. Does anyone know a way? 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.
[Freesurfer] Error map
Hi, I am looking for a tool of FreeSurfer. In fact, the tool is supposed to take in input 2 surfaces ( hemispheres) of subjects, registrate the surfaces and display the difference between the 2surfaces ( like 'euclidian distance'). What I want is exactly that output (http://www.sciencedirect.com/science/article/pii/S1053811909010064) availablein this article (http://www.sciencedirect.com/science/article/pii/S1053811909010064).Do you know the tool in question ?Thanks,VP ___ 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] Extract surface from volume
I have a volume in mnc and nii format. I would like to extract the outer surface from those volumes to be able to use in Freesurfer. I tried 'mri_vol2surf' but I didn't have the registration file. So I try make_register to create a registration file and the system give me an error as it couldn't open the header file to configure the fctstem...Does anyone know another way for extract the surface ( even with Matlab) ? Thanks, VP ___ 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] algorithm mris_anatomical_stats
Hi, Is it possible to get the algorithm of mris_anatomicacl_Stats. Just ot know which files it uses to compute metrics ... Thanks. VP___ 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] Brainsuite --> FreeSurfer
Hi bruce, I want cortical thickness, total surface area, instrinsec curvature index and folfing index. VP Date: Wed, 20 Mar 2013 13:09:54 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer it depends on what measures you want Bruce On Wed, 20 Mar 2013, Valtina Pouegue wrote: > Hi Bruces, > It's because i'm doing a comparison between brainsuite and freesrufer. So , I > would like to export results of > segmentation with Brainsuite and make measurements with FreeSurfer. In Fact, > with freesurfer I can have more parameters > than with freesurfer. > Does it exist another way for get measurements with surfaces ( not generated > by Freesurfer)? > Thx . > > VP > Date: Wed, 20 Mar 2013 08:38:26 -0400 > From: fis...@nmr.mgh.harvard.edu > To: pval...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer > > Hi Valtina > > you can try opening it with freeview if all you want is visualization. If > you are trying to produce anatomical stats you will need a lot more than > just the pial surface, as mris_anatomical_stats computes many things from > an array of inputs (such as the wm.mgz, the aseg.mgz, etc). Why not > just run recon-all and generate them? > Bruce > > > On Tue, 19 Mar 2013, Valtina Pouegue wrote: > > > I could see the created surface in MAtlab ( 'read_surf,) but I could't > > open the file in Freesurfer with tksurfer > > > > VP > > > > ___ > __ > > From: pval...@hotmail.com > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: Brainsuite --> FreeSurfer > > Date: Tue, 19 Mar 2013 22:34:39 -0400 > > > > Hi, > > > > I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like > > to get measurements with FreeSurfer. SO, I > > convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be > > usable with Freesurfer. Then, I tried to get > > measurements with the command .'mris_anatomical_stats' . with the file > > created previously in Matlab (I called it > > 'rh.pial'). But I got this error like the system is not able to read > > wm.mgz. > > That's why I thought I could juste replace th 'rh.pial' of the segmentation > > with Freesurfey by the 'rh.pial' created wi > th > > Matalb and then run mris_anatomical_Stats. IS this a good approximation. > > Could you recommand another way. > > > > > > VP > > > > > > ___ 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] Brainsuite --> FreeSurfer
Hi Bruces, It's because i'm doing a comparison between brainsuite and freesrufer. So , I would like to export results of segmentation with Brainsuite and make measurements with FreeSurfer. In Fact, with freesurfer I can have more parameters than with freesurfer. Does it exist another way for get measurements with surfaces ( not generated by Freesurfer)? Thx . VP Date: Wed, 20 Mar 2013 08:38:26 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer Hi Valtina you can try opening it with freeview if all you want is visualization. If you are trying to produce anatomical stats you will need a lot more than just the pial surface, as mris_anatomical_stats computes many things from an array of inputs (such as the wm.mgz, the aseg.mgz, etc). Why not just run recon-all and generate them? Bruce On Tue, 19 Mar 2013, Valtina Pouegue wrote: > I could see the created surface in MAtlab ( 'read_surf,) but I could't open > the file in Freesurfer with tksurfer > > VP > > _ > From: pval...@hotmail.com > To: freesurfer@nmr.mgh.harvard.edu > Subject: Brainsuite --> FreeSurfer > Date: Tue, 19 Mar 2013 22:34:39 -0400 > > Hi, > > I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like > to get measurements with FreeSurfer. SO, I > convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be > usable with Freesurfer. Then, I tried to get > measurements with the command .'mris_anatomical_stats' . with the file > created previously in Matlab (I called it > 'rh.pial'). But I got this error like the system is not able to read wm.mgz. > That's why I thought I could juste replace th 'rh.pial' of the segmentation > with Freesurfey by the 'rh.pial' created with > Matalb and then run mris_anatomical_Stats. IS this a good approximation. > Could you recommand another way. > > > VP > > ___ 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] Brainsuite --> FreeSurfer
I could see the created surface in MAtlab ( 'read_surf,) but I could't open the file in Freesurfer with tksurfer VP From: pval...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Brainsuite --> FreeSurfer Date: Tue, 19 Mar 2013 22:34:39 -0400 Hi, I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stats' . with the file created previously in Matlab (I called it 'rh.pial'). But I got this error like the system is not able to read wm.mgz.That's why I thought I could juste replace th 'rh.pial' of the segmentation with Freesurfey by the 'rh.pial' created with Matalb and then run mris_anatomical_Stats. IS this a good approximation. Could you recommand another way. VP ___ 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] Brainsuite --> FreeSurfer
Hi, I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stats' . with the file created previously in Matlab (I called it 'rh.pial'). But I got this error like the system is not able to read wm.mgz.That's why I thought I could juste replace th 'rh.pial' of the segmentation with Freesurfey by the 'rh.pial' created with Matalb and then run mris_anatomical_Stats. IS this a good approximation. Could you recommand another way. VP___ 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] Use a dfs file for measurements
Hi Freesurfers, I,ve done a segmentation with Brainsuite and as result I have dfs file for Pial surfaxe L/R hemisphere. I would like to do some measurement with mris_anatomical_stats of Freesurfers. But this fonction of FreeSurfer only accept surface of extension like ( .pial). How can I do this conversion ? Thanks . VP ___ 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_convert problem
Thanks a lot! Date: Fri, 15 Mar 2013 13:09:41 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem just: mri_convert volume.mgz cheers Bruce On Fri, 15 Mar 2013, Valtina Pouegue wrote: > Sorry, I am also a beginner in Linux environment. Now it works. > I try : > - > esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA > total 13892 > -rwxr--r-- 1 esther esther 14224696 12 mar 23:33 > t1_icbm_normal_1mm_pn3_rf20.mnc > [esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc > -rwxr--r-- 1 esther esther 14224696 12 mar > 23:33/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20. > mnc > > And this > -- > Volume information > for/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20. > mnc > type: MINC > dimensions: 181 x 217 x 181 >voxel sizes: 1., 1., 1. > type: SHORT (4) >fov: 217.000 >dof: 0 > xstart: -90.5, xend: 90.5 > ystart: -108.5, yend: 108.5 > zstart: -90.5, zend: 90.5 > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 > degrees >nframes: 1 >PhEncDir: UNKNOWN > ras xform present > xform info: x_r = 1., y_r = 0., z_r = 0., c_r = > 0.5000 > : x_a = 0., y_a = 1., z_a = 0., c_a = > -17.5000 > : x_s = 0., y_s = 0., z_s = 1., c_s = > 18.5000 > Orientation : RAS > Primary Slice Direction: axial > > voxel to ras transform: > 1. 0. 0. -90. > 0. 1. 0. -126. > 0. 0. 1. -72. > 0. 0. 0. 1. > > voxel-to-ras determinant 1 > > ras to voxel transform: > 1. -0. -0.90. >-0. 1. -0. 126. >-0. -0. 1.72. > 0. 0. 0. 1. > --- > > which command shoul I use for convert direct from MNC to mgz^ > > Thanks > > > Date: Fri, 15 Mar 2013 10:00:04 -0400 > From: fis...@nmr.mgh.harvard.edu > To: pval...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_convert problem > > can you run ls -l and mri_info on it? > On Fri, 15 Mar 2013, Valtina Pouegue > wrote: > > > I get this error- > > esther@m3012-04 ~]$ mri_info > > $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc > > mincRead(): can't find file/home/esther/Freesufer/freesurfer/subjects/AA/t > 1_icbm_normal_1mm_pn3_rf20.m > > nc > > ---I check in the directory enad the file is right there, > > > > > Date: Fri, 15 Mar 2013 09:24:22 -0400 > > > From: fis...@nmr.mgh.harvard.edu > > > To: pval...@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] mri_convert problem > > > > > > Hi Valtina > > > > > > you can convert directly without going through nii. What happens when yo > u > > > run ls -l on that file? Or mri_info? > > > > > > cheers > > > Bruce > > > > > > On Fri, 15 Mar 2013, Valtina Pouegue wrote: > > > > > > > Hi, > > > > > > > > I have a problem of conversion. I would like to convert mnc file to mg > z. > > But I think I shoul first convert mnc to nii then > > > > nii to mgz. , > > > > so I try the command mri_convert and I have this error; > > > > - > > > > [esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc > > Folder1.nii.gz > > > > mri_convert > > /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc > > Folder1.nii.gz > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > > > reading from > > /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc... > > > > mincRead(): can't find file > > /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc > > > > [esther@m3012-04 ~]$ > > > > > > > > I look up, and the file is at the rith place Could you help me.. > > > > Thanks > > > > > > > > VP] > > > > > > > > > > > > > > > > > The information
Re: [Freesurfer] mri_convert problem
Sorry, I am also a beginner in Linux environment. Now it works. I try :-esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AAtotal 13892-rwxr--r-- 1 esther esther 14224696 12 mar 23:33 t1_icbm_normal_1mm_pn3_rf20.mnc[esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc-rwxr--r-- 1 esther esther 14224696 12 mar 23:33 /home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.mncAnd this --Volume information for /home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.mnc type: MINCdimensions: 181 x 217 x 181 voxel sizes: 1., 1., 1. type: SHORT (4) fov: 217.000 dof: 0 xstart: -90.5, xend: 90.5ystart: -108.5, yend: 108.5 zstart: -90.5, zend: 90.5TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWNras xform presentxform info: x_r = 1., y_r = 0., z_r = 0., c_r = 0.5000 : x_a = 0., y_a = 1., z_a = 0., c_a = -17.5000 : x_s = 0., y_s = 0., z_s = 1., c_s =18.5000Orientation : RASPrimary Slice Direction: axial voxel to ras transform:1. 0. 0. -90. 0. 1. 0. -126.0. 0. 1. -72.0. 0. 0. 1. voxel-to-ras determinant 1 ras to voxel transform:1. -0. -0.90. -0. 1. -0. 126. -0. -0. 1.72.0. 0. 0. 1.--- which command shoul I use for convert direct from MNC to mgz^ Thanks Date: Fri, 15 Mar 2013 10:00:04 -0400 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem can you run ls -l and mri_info on it? On Fri, 15 Mar 2013, Valtina Pouegue wrote: > I get this error- > esther@m3012-04 ~]$ mri_info > $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc > mincRead(): can't find > file/home/esther/Freesufer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.m > nc > ---I check in the directory enad the file is right there, > > > Date: Fri, 15 Mar 2013 09:24:22 -0400 > > From: fis...@nmr.mgh.harvard.edu > > To: pval...@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] mri_convert problem > > > > Hi Valtina > > > > you can convert directly without going through nii. What happens when you > > run ls -l on that file? Or mri_info? > > > > cheers > > Bruce > > > > On Fri, 15 Mar 2013, Valtina Pouegue wrote: > > > > > Hi, > > > > > > I have a problem of conversion. I would like to convert mnc file to mgz. > But I think I shoul first convert mnc to nii then > > > nii to mgz. , > > > so I try the command mri_convert and I have this error; > > > - > > > [esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc > Folder1.nii.gz > > > mri_convert > /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc > Folder1.nii.gz > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > > reading from > /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc... > > > mincRead(): can't find file > /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc > > > [esther@m3012-04 ~]$ > > > > > > I look up, and the file is at the rith place Could you help me.. > > > Thanks > > > > > > VP] > > > > > > > > > > > > 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
Re: [Freesurfer] mri_convert problem
I get this error-esther@m3012-04 ~]$ mri_info $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mncmincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.mnc---I check in the directory enad the file is right there, > Date: Fri, 15 Mar 2013 09:24:22 -0400 > From: fis...@nmr.mgh.harvard.edu > To: pval...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_convert problem > > Hi Valtina > > you can convert directly without going through nii. What happens when you > run ls -l on that file? Or mri_info? > > cheers > Bruce > > On Fri, 15 Mar 2013, Valtina Pouegue wrote: > > > Hi, > > > > I have a problem of conversion. I would like to convert mnc file to mgz. > > But I think I shoul first convert mnc to nii then > > nii to mgz. , > > so I try the command mri_convert and I have this error; > > - > > [esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc > > Folder1.nii.gz > > mri_convert > > /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc > > Folder1.nii.gz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from > > /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc... > > mincRead(): can't find file > > /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc > > [esther@m3012-04 ~]$ > > > > I look up, and the file is at the rith place Could you help me.. > > Thanks > > > > VP] > > > > > > > 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] mri_convert problem
Hi, I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error; -[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gzmri_convert /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $reading from /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc...mincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc[esther@m3012-04 ~]$ I look up, and the file is at the rith place Could you help me..Thanks VP] ___ 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] Extract pial surface
Hi Freesurfers, I would like to extract the whole pial surface of a brain volume. I already done the segmentation and i have ( rh.pial and lh.pial surfaces). Does it exist a way to get the whole pial surface without separation? Thanks. VP ___ 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] Time
Just a dial error. I use the all at the end. I have 4 subjects and a set of dicom for each subjects. I would like to convert my dicoms files to be able to make a segmentation with Freesurfer ... Date: Fri, 8 Mar 2013 14:32:20 -0500 From: fis...@nmr.mgh.harvard.edu To: pval...@hotmail.com CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu; gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Time what are you trying to do? If run a recon, your first command should have a -all at the end of it cheers Bruce On Fri, 8 Mar 2013, Valtina Pouegue wrote: > I don't think the disk is a problem: I have a lot of space. But in resume, > here is exactly what i did ( in order):- I created a folder where I saved > the dicoms of my subject > - I tried the command > > recon-all -i [-i ] -s > > > like recon-all -i $SUBJECTS_DIR/PatientXX/blablabla.dcm -s XX . > - I got a folder with empty folders excepts orig which got a folder name > '001.mgz'. > - I thought that the file was .mgz was my dicom in .mgz, so I try opened > them with tkmedit , and It didn't work > - I also launch just after the recon-all command for segmentation . > - Just after I try the mri_convert for my subject like ' > mri_convert $SUBJECTS_DIR/PatientXX/blablabla.dcm out.mgz > - I got an mgz folder in the /mri/ > - I opened it with tkmedit and I could see the volume > > So, I retry with another subject , an I got the error described in the > previous mail. Did I make a mistake somewhere? > VP > > Date: Fri, 8 Mar 2013 14:19:29 -0500 > > From: fis...@nmr.mgh.harvard.edu > > To: pval...@hotmail.com > > CC: gr...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu; > ni...@nmr.mgh.harvard.edu > > Subject: RE: [Freesurfer] Time > > > > looks like you don't have permission to write to that directory (or the > > disk is full) > > > > On Fri, 8 Mar 2013, Valtina Pouegue wrote: > > > > > > > > VP,I try FreeView,, tit > > I dont really know what going on, i try mri-convert with another subject > > > aand i get this: > > > > > > [esther@IP132-207-67-224 /]$ mri_convert > > > $SUBJECTS_DIR/Patient3B/IM-0007--2095579184-0001.dcm out.mgz > > >mri_convert/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2 > 095579184-0 > > > 001.dcm out.mgz > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > > readingfrom/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--20955791 > 84-0 > > > 001.dcm... > > > Starting DICOMRead2() > > > dcmfile=/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2095579184- > 0 > > > 001.dcm > > > dcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient3B > > > Ref Series No = 9 > > > Found 22 files, checking for dicoms > > > Found 20 dicom files in series. > > > First Sorting > > > Computing Slice Direction > > > Vs: 0.260945 -0.596504 6.96965 > > > Vs: 0.0372779 -0.0852149 0.995665 > > > Second Sorting > > > Counting frames > > > nframes = 1 > > > nslices = 20 > > > ndcmfiles = 20 > > > PE Dir = ROW (dicom read) > > > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > > > Loading pixel data > > > TR=466.66, TE=9.00, TI=0.00, flip angle=90.00 > > > i_ras = (-0.9993, -0, -0.0374158) > > > j_ras = (-0.00317395, -0.996363, 0.0851462) > > > k_ras = (-0.0372779, 0.0852149, 0.995665) > > > writing to out.mgz... > > > mghWrite(out.mgz, -1): could not open file > > > ERROR: failure writing out.mgz > > > [esther@IP132-207-67-224 /]$ > > > -- > > > > > > I thiought that the software automatically created the out.mgz > > > > > > > Date: Fri, 8 Mar 2013 13:39:51 -0500 > > > > From: fis...@nmr.mgh.harvard.edu > > > > To: gr...@nmr.mgh.harvard.edu > > > > CC: pval...@hotmail.com; freesurfer@nmr.mgh.harvard.edu; > > > ni...@nmr.mgh.harvard.edu > > > > Subject: Re: [Freesurfer] Time > > > > > > > > or even > > > > > > > > freeview -v /path/to/dicomfile > > > > On Fri, 8 Mar 2013, Douglas N Greve wrote: > > > > > > > > > > > > > > No, you can just run tkmedit -f subject/mri/orig/001.mgz > > > > > You do not need to run recon-all to get a volume, you can just run > > > > > mri_convert, eg > > > > > mri_convert /path/to/dicomfile out.mgz > > > > > tkmedit -f
Re: [Freesurfer] Time
I don't think the disk is a problem: I have a lot of space. But in resume, here is exactly what i did ( in order):- I created a folder where I saved the dicoms of my subject- I tried the command recon-all -i [-i ] -s like recon-all -i $SUBJECTS_DIR/PatientXX/blablabla.dcm -s XX . - I got a folder with empty folders excepts orig which got a folder name '001.mgz'.- I thought that the file was .mgz was my dicom in .mgz, so I try opened them with tkmedit , and It didn't work- I also launch just after the recon-all command for segmentation .- Just after I try the mri_convert for my subject like ' mri_convert $SUBJECTS_DIR/PatientXX/blablabla.dcm out.mgz- I got an mgz folder in the /mri/- I opened it with tkmedit and I could see the volume So, I retry with another subject , an I got the error described in the previous mail. Did I make a mistake somewhere? VP Date: Fri, 8 Mar 2013 14:19:29 -0500 > From: fis...@nmr.mgh.harvard.edu > To: pval...@hotmail.com > CC: gr...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu; > ni...@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Time > > looks like you don't have permission to write to that directory (or the > disk is full) > > On Fri, 8 Mar 2013, Valtina Pouegue wrote: > > > > > VP,I try FreeView,, tit > I dont really know what going on, i try mri-convert with another subject > > aand i get this: > > > > [esther@IP132-207-67-224 /]$ mri_convert > > $SUBJECTS_DIR/Patient3B/IM-0007--2095579184-0001.dcm out.mgz > > mri_convert/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2095579184-0 > > 001.dcm out.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading > > from/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2095579184-0 > > 001.dcm... > > Starting DICOMRead2() > > dcmfile > > =/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2095579184-0 > > 001.dcm > > dcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient3B > > Ref Series No = 9 > > Found 22 files, checking for dicoms > > Found 20 dicom files in series. > > First Sorting > > Computing Slice Direction > > Vs: 0.260945 -0.596504 6.96965 > > Vs: 0.0372779 -0.0852149 0.995665 > > Second Sorting > > Counting frames > > nframes = 1 > > nslices = 20 > > ndcmfiles = 20 > > PE Dir = ROW (dicom read) > > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > > Loading pixel data > > TR=466.66, TE=9.00, TI=0.00, flip angle=90.00 > > i_ras = (-0.9993, -0, -0.0374158) > > j_ras = (-0.00317395, -0.996363, 0.0851462) > > k_ras = (-0.0372779, 0.0852149, 0.995665) > > writing to out.mgz... > > mghWrite(out.mgz, -1): could not open file > > ERROR: failure writing out.mgz > > [esther@IP132-207-67-224 /]$ > > -- > > > > I thiought that the software automatically created the out.mgz > > > > > Date: Fri, 8 Mar 2013 13:39:51 -0500 > > > From: fis...@nmr.mgh.harvard.edu > > > To: gr...@nmr.mgh.harvard.edu > > > CC: pval...@hotmail.com; freesurfer@nmr.mgh.harvard.edu; > > ni...@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Time > > > > > > or even > > > > > > freeview -v /path/to/dicomfile > > > On Fri, 8 Mar 2013, Douglas N Greve wrote: > > > > > > > > > > > No, you can just run tkmedit -f subject/mri/orig/001.mgz > > > > You do not need to run recon-all to get a volume, you can just run > > > > mri_convert, eg > > > > mri_convert /path/to/dicomfile out.mgz > > > > tkmedit -f out.mgz > > > > > > > > doug > > > > > > > > On 03/08/2013 12:54 PM, Valtina Pouegue wrote: > > > >> If i'm right, the command: > recon-all -s 13A -all execute the whole > > > >> segmentation ( between 20-40 hours). > > > >> So , if I just want the see the volume, I have to to the segmentation > > > >> [ absolutely] ? > > > >> VP > > > >> > > > >>> Date: Fri, 8 Mar 2013 12:36:34 -0500 > > > >>> From: gr...@nmr.mgh.harvard.edu > > > >>> To: pval...@hotmail.com > > > >>> CC: freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu > > > >>> Subject: Re: [Freesurfer] Time > > > >>> > > > >>> You will need to run the full processing stream. You can do that from > > > >>> the beginning with > > > >>> > > > >>
Re: [Freesurfer] Time
VP,I try FreeView,, tit Date: Fri, 8 Mar 2013 13:39:51 -0500 > From: fis...@nmr.mgh.harvard.edu > To: gr...@nmr.mgh.harvard.edu > CC: pval...@hotmail.com; freesurfer@nmr.mgh.harvard.edu; > ni...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Time > > or even > > freeview -v /path/to/dicomfile > On Fri, 8 Mar 2013, Douglas N Greve wrote: > > > > > No, you can just run tkmedit -f subject/mri/orig/001.mgz > > You do not need to run recon-all to get a volume, you can just run > > mri_convert, eg > > mri_convert /path/to/dicomfile out.mgz > > tkmedit -f out.mgz > > > > doug > > > > On 03/08/2013 12:54 PM, Valtina Pouegue wrote: > >> If i'm right, the command: > recon-all -s 13A -all execute the whole > >> segmentation ( between 20-40 hours). > >> So , if I just want the see the volume, I have to to the segmentation > >> [ absolutely] ? > >> VP > >> > >>> Date: Fri, 8 Mar 2013 12:36:34 -0500 > >>> From: gr...@nmr.mgh.harvard.edu > >>> To: pval...@hotmail.com > >>> CC: freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu > >>> Subject: Re: [Freesurfer] Time > >>> > >>> You will need to run the full processing stream. You can do that from > >>> the beginning with > >>> > >>> recon-all -i $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s > >>> 13A -all > >>> > >>> but now that you have a file there, you can run > >>> > >>> recon-all -s 13A -all > >>> > >>> doug > >>> > >>> > >>> On 03/08/2013 12:31 PM, Valtina Pouegue wrote: > >>>> I convert my set of DICOM of the folder 'Patient13A' > >>>> > >>>> [esther@IP132-207-67-224 ~]$ recon-all -i > >>>> $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s 13A > >>>> Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > >>>> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > >>>> INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjects > >>>> Actual FREESURFER_HOME /home/esther/Freesurfer/freesurfer > >>>> Linux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 19 22:54:16 > >>>> UTC 2012 x86_64 x86_64 x86_64 GNU/Linux > >>>> /home/esther/Freesurfer/freesurfer/subjects/13A > >>>> > >>>> mri_convert > >>>> > >> /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm > >> > >>>> /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz > >>>> > >>>> mri_convert > >>>> > >> /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm > >> > >>>> /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz > >>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > >>>> reading from > >>>> > >> /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm... > >>>> Starting DICOMRead2() > >>>> dcmfile = > >>>> > >> /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm > >>>> dcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient13A > >>>> Ref Series No = 7 > >>>> Found 23 files, checking for dicoms > >>>> Found 21 dicom files in series. > >>>> First Sorting > >>>> Computing Slice Direction > >>>> Vs: -0.598129 1.13977 6.88063 > >>>> Vs: -0.0854471 0.162824 0.982948 > >>>> Second Sorting > >>>> Counting frames > >>>> nframes = 1 > >>>> nslices = 21 > >>>> ndcmfiles = 21 > >>>> PE Dir = ROW (dicom read) > >>>> TransferSyntaxUID: --1.2.840.10008.1.2.1-- > >>>> Loading pixel data > >>>> TR=500.00, TE=9.00, TI=0.00, flip angle=90.00 > >>>> i_ras = (-0.992199, 0.0759614, 0.0988506) > >>>> j_ras = (-0.0907614, -0.983726, -0.155063) > >>>> k_ras = (0.0854471, -0.162824, 0.982948) > >>>> writing to > >>>> /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz... > >>>> > >>>> #-- > >>>> > >>>> recon-all -s 13A finished without
Re: [Freesurfer] Time
OK. Thanks ! ;) > Date: Fri, 8 Mar 2013 13:16:10 -0500 > From: gr...@nmr.mgh.harvard.edu > To: pval...@hotmail.com > CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Time > > > No, you can just run tkmedit -f subject/mri/orig/001.mgz > You do not need to run recon-all to get a volume, you can just run > mri_convert, eg > mri_convert /path/to/dicomfile out.mgz > tkmedit -f out.mgz > > doug > > On 03/08/2013 12:54 PM, Valtina Pouegue wrote: > > If i'm right, the command: > recon-all -s 13A -all execute the whole > > segmentation ( between 20-40 hours). > > So , if I just want the see the volume, I have to to the segmentation > > [ absolutely] ? > > VP > > > > > Date: Fri, 8 Mar 2013 12:36:34 -0500 > > > From: gr...@nmr.mgh.harvard.edu > > > To: pval...@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Time > > > > > > You will need to run the full processing stream. You can do that from > > > the beginning with > > > > > > recon-all -i $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s > > > 13A -all > > > > > > but now that you have a file there, you can run > > > > > > recon-all -s 13A -all > > > > > > doug > > > > > > > > > On 03/08/2013 12:31 PM, Valtina Pouegue wrote: > > > > I convert my set of DICOM of the folder 'Patient13A' > > > > > > > > [esther@IP132-207-67-224 ~]$ recon-all -i > > > > $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s 13A > > > > Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > > > > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > > > > INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjects > > > > Actual FREESURFER_HOME /home/esther/Freesurfer/freesurfer > > > > Linux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 19 22:54:16 > > > > UTC 2012 x86_64 x86_64 x86_64 GNU/Linux > > > > /home/esther/Freesurfer/freesurfer/subjects/13A > > > > > > > > mri_convert > > > > > > /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm > > > > > > > > /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz > > > > > > > > mri_convert > > > > > > /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm > > > > > > > > /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > > > reading from > > > > > > /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm... > > > > Starting DICOMRead2() > > > > dcmfile = > > > > > > /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm > > > > dcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient13A > > > > Ref Series No = 7 > > > > Found 23 files, checking for dicoms > > > > Found 21 dicom files in series. > > > > First Sorting > > > > Computing Slice Direction > > > > Vs: -0.598129 1.13977 6.88063 > > > > Vs: -0.0854471 0.162824 0.982948 > > > > Second Sorting > > > > Counting frames > > > > nframes = 1 > > > > nslices = 21 > > > > ndcmfiles = 21 > > > > PE Dir = ROW (dicom read) > > > > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > > > > Loading pixel data > > > > TR=500.00, TE=9.00, TI=0.00, flip angle=90.00 > > > > i_ras = (-0.992199, 0.0759614, 0.0988506) > > > > j_ras = (-0.0907614, -0.983726, -0.155063) > > > > k_ras = (0.0854471, -0.162824, 0.982948) > > > > writing to > > > > /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz... > > > > > > > > #-- > > > > > > > > recon-all -s 13A finished without error at Fri Mar 8 11:37:30 EST 2013 > > > > done > > > > -- > > > > After i executed the tkmedit.. > > > > VP > > > > > Date: Fri, 8 Mar 2013 12:26:14 -0500 > > > > > From: gr...@nmr.mgh.harvard.edu > > > > > To: pval...@hotmail.com >
Re: [Freesurfer] Time
If i'm right, the command: > recon-all -s 13A -all execute the whole segmentation ( between 20-40 hours). So , if I just want the see the volume, I have to to the segmentation [ absolutely] ?VP > Date: Fri, 8 Mar 2013 12:36:34 -0500 > From: gr...@nmr.mgh.harvard.edu > To: pval...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Time > > You will need to run the full processing stream. You can do that from > the beginning with > > recon-all -i $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s > 13A -all > > but now that you have a file there, you can run > > recon-all -s 13A -all > > doug > > > On 03/08/2013 12:31 PM, Valtina Pouegue wrote: > > I convert my set of DICOM of the folder 'Patient13A' > > > > [esther@IP132-207-67-224 ~]$ recon-all -i > > $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s 13A > > Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > > INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjects > > Actual FREESURFER_HOME /home/esther/Freesurfer/freesurfer > > Linux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 19 22:54:16 > > UTC 2012 x86_64 x86_64 x86_64 GNU/Linux > > /home/esther/Freesurfer/freesurfer/subjects/13A > > > > mri_convert > > /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm > > > > /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz > > > > mri_convert > > /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm > > > > /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from > > /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm... > > Starting DICOMRead2() > > dcmfile = > > /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm > > dcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient13A > > Ref Series No = 7 > > Found 23 files, checking for dicoms > > Found 21 dicom files in series. > > First Sorting > > Computing Slice Direction > > Vs: -0.598129 1.13977 6.88063 > > Vs: -0.0854471 0.162824 0.982948 > > Second Sorting > > Counting frames > > nframes = 1 > > nslices = 21 > > ndcmfiles = 21 > > PE Dir = ROW (dicom read) > > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > > Loading pixel data > > TR=500.00, TE=9.00, TI=0.00, flip angle=90.00 > > i_ras = (-0.992199, 0.0759614, 0.0988506) > > j_ras = (-0.0907614, -0.983726, -0.155063) > > k_ras = (0.0854471, -0.162824, 0.982948) > > writing to > > /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz... > > > > #-- > > > > recon-all -s 13A finished without error at Fri Mar 8 11:37:30 EST 2013 > > done > > ------ > > After i executed the tkmedit.. > > VP > > > Date: Fri, 8 Mar 2013 12:26:14 -0500 > > > From: gr...@nmr.mgh.harvard.edu > > > To: pval...@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] Time > > > > > > Does that file exist? What was your command to create the mgz file? > > > On 03/08/2013 12:12 PM, Valtina Pouegue wrote: > > > > Hi, > > > > I convert my files and i get news folders with one file with the > > > > extension .mgz in the folder orig. But , when i try to loasd the > > > > volume, I get an error > > > > - > > > > [esther@IP132-207-67-224 ~]$ tkmedit 13A orig.mgz > > > > mghRead(/home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig.mgz, > > > > -1): could not open file > > > > > > > > > > > > Error: Loading volume orig.mgz > > > > > > > > Couldn't read the anatomical volume. > > > > > > > > Tkmedit couldn't read the volume you specified. > > > > This could be because the image format wasn't recognized, > > > > or it couldn't find the proper header, > > > > or the file(s) were unreadable, > > > > or it was the wrong size. > > > > --- > > > > > > > > could you please help me ? > > > > > > > > VP > &
Re: [Freesurfer] Time
I convert my set of DICOM of the folder 'Patient13A'[esther@IP132-207-67-224 ~]$ recon-all -i $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s 13ASubject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjectsActual FREESURFER_HOME /home/esther/Freesurfer/freesurferLinux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 19 22:54:16 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux/home/esther/Freesurfer/freesurfer/subjects/13A mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $reading from /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcm...Starting DICOMRead2()dcmfile = /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-0001.dcmdcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient13ARef Series No = 7Found 23 files, checking for dicomsFound 21 dicom files in series.First SortingComputing Slice DirectionVs: -0.598129 1.13977 6.88063Vs: -0.0854471 0.162824 0.982948Second SortingCounting framesnframes = 1nslices = 21ndcmfiles = 21PE Dir = ROW (dicom read)TransferSyntaxUID: --1.2.840.10008.1.2.1--Loading pixel dataTR=500.00, TE=9.00, TI=0.00, flip angle=90.00i_ras = (-0.992199, 0.0759614, 0.0988506)j_ras = (-0.0907614, -0.983726, -0.155063)k_ras = (0.0854471, -0.162824, 0.982948)writing to /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz... #-- recon-all -s 13A finished without error at Fri Mar 8 11:37:30 EST 2013done--After i executed the tkmedit..VP > Date: Fri, 8 Mar 2013 12:26:14 -0500 > From: gr...@nmr.mgh.harvard.edu > To: pval...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Time > > Does that file exist? What was your command to create the mgz file? > On 03/08/2013 12:12 PM, Valtina Pouegue wrote: > > Hi, > > I convert my files and i get news folders with one file with the > > extension .mgz in the folder orig. But , when i try to loasd the > > volume, I get an error > > - > > [esther@IP132-207-67-224 ~]$ tkmedit 13A orig.mgz > > mghRead(/home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig.mgz, > > -1): could not open file > > > > > > Error: Loading volume orig.mgz > > > > Couldn't read the anatomical volume. > > > > Tkmedit couldn't read the volume you specified. > > This could be because the image format wasn't recognized, > > or it couldn't find the proper header, > > or the file(s) were unreadable, > > or it was the wrong size. > > --- > > > > could you please help me ? > > > > VP > > > > > > From: ni...@nmr.mgh.harvard.edu > > Date: Thu, 7 Mar 2013 21:11:31 -0500 > > To: pval...@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu; gr...@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Time > > > > yes, if you give it the filename of the first .dcm in the series, the > > software will find the other slices and create the .mgz. > > > > > > > > On Mar 7, 2013, at 9:02 PM, Valtina Pouegue > <mailto:pval...@hotmail.com>> wrote: > > > > Oh yes. It's my mistake. But should I give the adress of the first > > file of my set for having the result in .mgz. > > Thanks. > > > > > > > Date: Thu, 7 Mar 2013 16:00:53 -0500 > > > From: gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > > To: pval...@hotmail.com <mailto:pval...@hotmail.com>; > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] Time > > > > > > You cannot give recon-all a folder as input. It must be an image > > file. > > > If you have multiple files, you need multiple -i flags. > > > doug > > > > > > > > > On 03/07/2013 03:48 PM, Valtina Pouegue wrote: > > > > Hi, > > > > Here it is > > > > [esther@IP132-207-67-224 ~]$ recon-all -i > > > > /home/esther/Frees
Re: [Freesurfer] Time
Hi, I convert my files and i get news folders with one file with the extension .mgz in the folder orig. But , when i try to loasd the volume, I get an error -[esther@IP132-207-67-224 ~]$ tkmedit 13A orig.mgzmghRead(/home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig.mgz, -1): could not open file Error: Loading volume orig.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.--- could you please help me ? VP From: ni...@nmr.mgh.harvard.edu Date: Thu, 7 Mar 2013 21:11:31 -0500 To: pval...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Time yes, if you give it the filename of the first .dcm in the series, the software will find the other slices and create the .mgz. On Mar 7, 2013, at 9:02 PM, Valtina Pouegue wrote: Oh yes. It's my mistake. But should I give the adress of the first file of my set for having the result in .mgz. Thanks. > Date: Thu, 7 Mar 2013 16:00:53 -0500 > From: gr...@nmr.mgh.harvard.edu > To: pval...@hotmail.com; Freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Time > > You cannot give recon-all a folder as input. It must be an image file. > If you have multiple files, you need multiple -i flags. > doug > > > On 03/07/2013 03:48 PM, Valtina Pouegue wrote: > > Hi, > > Here it is > > [esther@IP132-207-67-224 ~]$ recon-all -i > > /home/esther/Freesurfer/freesurfer/subjects/Patient13B -s 13B > > Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > > INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjects > > Actual FREESURFER_HOME /home/esther/Freesurfer/freesurfer > > Linux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 19 22:54:16 > > UTC 2012 x86_64 x86_64 x86_64 GNU/Linux > > /home/esther/Freesurfer/freesurfer/subjects/13B > > > > mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13B > > /home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz > > > > mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13B > > /home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz > > corRead(): can't open file > > /home/esther/Freesurfer/freesurfer/subjects/Patient13B/COR-.info > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from /home/esther/Freesurfer/freesurfer/subjects/Patient13B... > > > > VP > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer 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 y
Re: [Freesurfer] Time
Oh yes. It's my mistake. But should I give the adress of the first file of my set for having the result in .mgz. Thanks. > Date: Thu, 7 Mar 2013 16:00:53 -0500 > From: gr...@nmr.mgh.harvard.edu > To: pval...@hotmail.com; Freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Time > > You cannot give recon-all a folder as input. It must be an image file. > If you have multiple files, you need multiple -i flags. > doug > > > On 03/07/2013 03:48 PM, Valtina Pouegue wrote: > > Hi, > > Here it is > > [esther@IP132-207-67-224 ~]$ recon-all -i > > /home/esther/Freesurfer/freesurfer/subjects/Patient13B -s 13B > > Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > > INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjects > > Actual FREESURFER_HOME /home/esther/Freesurfer/freesurfer > > Linux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 19 22:54:16 > > UTC 2012 x86_64 x86_64 x86_64 GNU/Linux > > /home/esther/Freesurfer/freesurfer/subjects/13B > > > > mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13B > > /home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz > > > > mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13B > > /home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz > > corRead(): can't open file > > /home/esther/Freesurfer/freesurfer/subjects/Patient13B/COR-.info > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from /home/esther/Freesurfer/freesurfer/subjects/Patient13B... > > > > VP > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Time
Hi, I have 8 folders of 26 slice odf dicom. Yesterday, I launched the conversion to .mgz with the command recon-all -i [-i ] -s . All my folders are created but in the Orig folder I don't fige files .mgz. I think that the processing time is really long but I'm not sure. Do you know somthing about? Thanks. VP___ 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] Extract cortex surface with Freesurfer
Hi, I'm a new user of Freesurfer. 1) I would like to extract only the cortex cerebrum . So I think I don't need the complete subcortical segmentation ( 20-40 hours). Do you know a way to segment only cortex or only ( cortex+ pial ( left/rigt hemispher)?2) I already try the complete subcortical segmentation ( about 12 hours, with the recon-all command). Do you know a way to extract only the cortex surface from the software? I would like to get the 3D surface mesh for analysis on Matlab. Could you help me, Thanks. VP. ___ 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.
