Re: [Freesurfer] permission denied
Hi Z K, Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one installed with the latest freesurfer version did not work while others finished the processing in a reasonable processing time and I got the results. Also, I have a PC at my office installed with the latest freesurfer version and it works fine. So I have two PCs installed with the latest Freesurfer (one of them which does not work is in the lab). To summarize: All PCs (16 PCs in the lab and 1 in my office) are installed with latest Ubuntu version 14.04 64 bits 15 PCs in the lab are installed with freesurfer 5.0.0 version 1 PC in the lab is installed with the latest freesurfer version (does not work, permission denied) 1 PC in my office is installed with the latest freesurfer version (works fine) All these PCs have Ubuntu 14.04 64bit installed on them. No, I am not using any vitual machine. Regarding the root user, I will try it on Sunday as I am away for a couple of days. Many thanks for your continuous support. Ali On Thu, Oct 30, 2014 at 6:34 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Ali, First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are working properly? I am under the impression that versions of freesurfer pre-version 5.3 will not work on newer linux distributions? In regards to your current permision denied issue... What happens if you try and run tkmedit as root user? Also, you not using virtual machine setup are you? -Zeke On 10/30/2014 06:27 AM, Ali Radaideh wrote: It does not work. This is really strange On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: I beleive it should have a lower case X, as in: chmod -R a+x freesurfer/bin -Zeke On 10/28/2014 01:19 AM, Ali Radaideh wrote: Dear Douglas Thanks for your reply. unfortunatey I still get the same error. Here is the terminal output. Is there anything else I can do? freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl imaging@imaging-ThinkCentre-23:~$ tcsh imaging-ThinkCentre-23:~ tkmedit /usr/local/freesurfer/bin/tkmedit: Permission denied. imaging-ThinkCentre-23:~ On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Try chmod -R a+X freesurfer/bin On 10/26/14 1:57 PM, Ali Radaideh wrote: Dear FreeSurfer users, I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I try a command such such as tkmedit i get the following error /usr/local/freesurfer/bin/tkmedit: permission denied. I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer but did not work. Any ideas why is this happening although I have done the same thing to other PCs and they are working fine. Thanks in advance, Ali -- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 390 ext.5422, 5355, 5364 Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] White matter volume
Hi Bruce, I wanted to calculate the right and left hemispheric white matter volume using a mask. Is there any difference between lh.dwhite.mgz , rh.dwhite.mgz (the outputs of mris_volmmask after binarize them) and the right and left hemispheric white matter masks from aseg.mgz atlas (the output of mri_binarize command line)? I am asking this question because those masks gave me different estimation for the volume? Thanks! Mohamad ___ 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] White matter volume
The aseg is not surface-based and will not be as accurate doug On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote: Hi Bruce, I wanted to calculate the right and left hemispheric white matter volume using a mask. Is there any difference between lh.dwhite.mgz , rh.dwhite.mgz (the outputs of mris_volmmask after binarize them) and the right and left hemispheric white matter masks from aseg.mgz atlas (the output of mri_binarize command line)? I am asking this question because those masks gave me different estimation for the volume? Thanks! Mohamad ___ 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] Longitudinal prediction
--osgm is for one-sample group mean which is the simplest design possible. It is probably not appropriate for your design. If you have different inputs and different labels then you will get different results On 10/30/2014 03:08 PM, Alex Hanganu wrote: Hi Martin, could you please confirm whether the glm analysis was correctly performed ? the command line is: /mri_glmfit --glmdir DIR --y lh.thickness-pc1.stack.fwhm15.mgh //--label lh.fsaverage.cortex.label //--fsgd FSGD_FILE --C Contrast-010..0.mtx --surf fsaverage lh / I get results, but I when I do the same command for the analysis from the 2-stage-model webpage, the results are different. For example, on the webpage the cmd is: /mri_glmfit --osgm --glmdir DIR --y Y.mgh --label LABEL.label --surf fsaverage lh/ I tried to receive the same result with: /mri_glmfit --glmdir DIR --y Y.mgh //--label LABEL.label //--fsgd FSGD_FILE --C Contrast-100...0.mtx --surf fsaverage lh / but the results are different. In this case, how can I be sure that the first analysis was performed correctly ? the /fsgd/ file was constructed using the base-subjects and the values were taken as in the /cross/ file that is used by qdec. Thanks, Alex On Thursday, October 23, 2014 2:52 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Alex, you are not looking at a one sample group mean (osgd) so don't pass that flag. Your design is probably something like 1 A other_co_vars_to_regress_out (these are column vectors). so contrast in that case would be [ 0 1 0... ] That should create all outputs. All of this is really cross sectional analysis where the depending variable is simply the 'change in thickness' instead of thickness itself. Take a look at the glm tutorial on the wiki, which describes the process. Best, Martin On 10/23/2014 02:40 PM, Alex Hanganu wrote: Hi Martin, thanks for confirming. I duplicated the parameter and got good results in qdec. I also tried to repeat the analysis with mri_glmfit but I can't manage to come to an end. In order to analyse the correlation between pc1 and parameter 'A', it seems that I have to construct an fsgd file, that is different from the .qdec file included in the long_mris_slopes command. Nevertheless, after doing so (presumably all Inputs were attibuted to subject.long.base-time1 and subject.long.base-time2) I thought that a contrast is needed, yet the --C and the --osgm flags cannot be used together. - How can the correlation between -pc1 and parameter 'A' be performed in this case ? Additionally, after performing the mri_glmfit described in the 2-stage-model page, in the tksurfer how can I see the plot ? The y.fsgd file wasn't created. Is there another method ? Thanks, Alex Le mardi 21 octobre 2014 16h40, Martin Reuter mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu a écrit : Hi Alex, you have to duplicate the parameter (it is basically fixed across time). If you put 0 for tp2, it will average the two values, which is not what you want. Otherwise I think it is the correct approach. Best, Martin On 10/21/2014 04:31 PM, Alex Hanganu wrote: Dear Martin, thank you very much for your answer ! and thanks for all the details ! - yes, we have exactly 2 time points in all subjects and the parameter is a single number. In qdec - it seems that qdec table has to include the parameter 'A' both at time 1 and at time 2 in order for long_qdec_table command to create the cross file. I put a zero at time 2. In qdec design we analyzed parameter 'A' with -pc1 and -spc. I'm not sure that this is the correct approach. I'll continue with LME and mri_glmfit. Sincerely, Alex Le mardi 21 octobre 2014 9h19, Martin Reuter mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu a écrit : Hi Alex, the parameter is a single number that happens to be measured at time 1 right, eg baseline age? Lets call that parameter 'A' for the discussion below. Also you have exactly 2 time points in all subjects? There is two alternatives: 1. Simple approach (2-stage-model): You compute the atrophy rate (e.g. percent thickness change) on the cortex (long_mris_slopes) for each subject. At this point you have 1 measure per subject and work cross-sectionally. You can use qdec or mri_glmfit to correlate 'A' (independent parameter) with the thickness change (dependent variable). This is OK if you have the same number of time points and the same time distance in all subjects. Details here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel 2. Better approach: use Linear Mixed Effects models (we have matlab tools for that). This model is more flexible (different manycolumn of ones, time points, different time intervals, even subjects with a single time point can be added). You'd setup a system like Y_ij = beta_0 + b_i + beta_1 * A_i + beta_2 t_ij + beta_3 A_i *
Re: [Freesurfer] White matter volume
Thanks Doug! So do you suggest to use lh.dwhite.mgz , rh.dwhite.mgz the output of mris_volmask? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 10:02 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter volume The aseg is not surface-based and will not be as accurate doug On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote: Hi Bruce, I wanted to calculate the right and left hemispheric white matter volume using a mask. Is there any difference between lh.dwhite.mgz , rh.dwhite.mgz (the outputs of mris_volmmask after binarize them) and the right and left hemispheric white matter masks from aseg.mgz atlas (the output of mri_binarize command line)? I am asking this question because those masks gave me different estimation for the volume? Thanks! Mohamad ___ 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] Longitudinal prediction
I see. Thank you Doug ! Now I used the command lines from the qdec output in the terminal and I constructed the next contrasts using them as a starting point. Now the results seem more reliable and I can perform the Monte-Carlo with 5000 iterations. I'll verify them once again with LME. Alex. On Friday, October 31, 2014 10:05 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: --osgm is for one-sample group mean which is the simplest design possible. It is probably not appropriate for your design. If you have different inputs and different labels then you will get different results On 10/30/2014 03:08 PM, Alex Hanganu wrote: Hi Martin, could you please confirm whether the glm analysis was correctly performed ? the command line is: /mri_glmfit --glmdir DIR --y lh.thickness-pc1.stack.fwhm15.mgh //--label lh.fsaverage.cortex.label //--fsgd FSGD_FILE --C Contrast-010..0.mtx --surf fsaverage lh / I get results, but I when I do the same command for the analysis from the 2-stage-model webpage, the results are different. For example, on the webpage the cmd is: /mri_glmfit --osgm --glmdir DIR --y Y.mgh --label LABEL.label --surf fsaverage lh/ I tried to receive the same result with: /mri_glmfit --glmdir DIR --y Y.mgh //--label LABEL.label //--fsgd FSGD_FILE --C Contrast-100...0.mtx --surf fsaverage lh / but the results are different. In this case, how can I be sure that the first analysis was performed correctly ? the /fsgd/ file was constructed using the base-subjects and the values were taken as in the /cross/ file that is used by qdec. Thanks, Alex On Thursday, October 23, 2014 2:52 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Alex, you are not looking at a one sample group mean (osgd) so don't pass that flag. Your design is probably something like 1 A other_co_vars_to_regress_out (these are column vectors). so contrast in that case would be [ 0 1 0... ] That should create all outputs. All of this is really cross sectional analysis where the depending variable is simply the 'change in thickness' instead of thickness itself. Take a look at the glm tutorial on the wiki, which describes the process. Best, Martin On 10/23/2014 02:40 PM, Alex Hanganu wrote: Hi Martin, thanks for confirming. I duplicated the parameter and got good results in qdec. I also tried to repeat the analysis with mri_glmfit but I can't manage to come to an end. In order to analyse the correlation between pc1 and parameter 'A', it seems that I have to construct an fsgd file, that is different from the .qdec file included in the long_mris_slopes command. Nevertheless, after doing so (presumably all Inputs were attibuted to subject.long.base-time1 and subject.long.base-time2) I thought that a contrast is needed, yet the --C and the --osgm flags cannot be used together. - How can the correlation between -pc1 and parameter 'A' be performed in this case ? Additionally, after performing the mri_glmfit described in the 2-stage-model page, in the tksurfer how can I see the plot ? The y.fsgd file wasn't created. Is there another method ? Thanks, Alex Le mardi 21 octobre 2014 16h40, Martin Reuter mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu a écrit : Hi Alex, you have to duplicate the parameter (it is basically fixed across time). If you put 0 for tp2, it will average the two values, which is not what you want. Otherwise I think it is the correct approach. Best, Martin On 10/21/2014 04:31 PM, Alex Hanganu wrote: Dear Martin, thank you very much for your answer ! and thanks for all the details ! - yes, we have exactly 2 time points in all subjects and the parameter is a single number. In qdec - it seems that qdec table has to include the parameter 'A' both at time 1 and at time 2 in order for long_qdec_table command to create the cross file. I put a zero at time 2. In qdec design we analyzed parameter 'A' with -pc1 and -spc. I'm not sure that this is the correct approach. I'll continue with LME and mri_glmfit. Sincerely, Alex Le mardi 21 octobre 2014 9h19, Martin Reuter mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu a écrit : Hi Alex, the parameter is a single number that happens to be measured at time 1 right, eg baseline age? Lets call that parameter 'A' for the discussion below. Also you have exactly 2 time points in all subjects? There is two alternatives: 1. Simple approach (2-stage-model): You compute the atrophy rate (e.g. percent thickness change) on the cortex (long_mris_slopes) for each subject. At this point you have 1 measure per subject and work cross-sectionally. You can use qdec or mri_glmfit to correlate 'A' (independent parameter) with the thickness change (dependent variable). This is OK if you have the same number of time points and the same time distance in all subjects. Details here:
Re: [Freesurfer] White matter volume
I would suggest using the value in aseg.stats. Is that not possible? On 10/31/2014 10:06 AM, Alshikho, Mohamad J. wrote: Thanks Doug! So do you suggest to use lh.dwhite.mgz , rh.dwhite.mgz the output of mris_volmask? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 10:02 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter volume The aseg is not surface-based and will not be as accurate doug On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote: Hi Bruce, I wanted to calculate the right and left hemispheric white matter volume using a mask. Is there any difference between lh.dwhite.mgz , rh.dwhite.mgz (the outputs of mris_volmmask after binarize them) and the right and left hemispheric white matter masks from aseg.mgz atlas (the output of mri_binarize command line)? I am asking this question because those masks gave me different estimation for the volume? Thanks! Mohamad ___ 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 -- 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] White matter volume
Hi Mohamad this is probably due to the partial-volume correction that we typically compute when we estimate volumes in the stats files. cheers Bruce On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote: Thanks Doug, In order to improve my understanding for the analysis that I am working on and in the process of my learning I am tring to calculate the volume in many different ways. Actually It is very easy, simple and possible to use the numbers mentioned in aseg.stats but what if we got different results when we use different methods? I caclated the right and left hemispheric white matter volume in FSL using a mask deriverd from the T1 segmentation in Freesurfer lh.dwhite.mgz , rh.dwhite.mgz then I binarized those masks and I registered them to my T1 then I used the command line fslstats T1 -k my mask -V What surprised me is that the volume was totally different from the one mentioned in aseg.stats (attached) I highly appreciate any advice. looking forward to learn from you Mohamad From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 11:04 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter volume I would suggest using the value in aseg.stats. Is that not possible? On 10/31/2014 10:06 AM, Alshikho, Mohamad J. wrote: Thanks Doug! So do you suggest to use lh.dwhite.mgz , rh.dwhite.mgz the output of mris_volmask? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 10:02 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter volume The aseg is not surface-based and will not be as accurate doug On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote: Hi Bruce, I wanted to calculate the right and left hemispheric white matter volume using a mask. Is there any difference between lh.dwhite.mgz , rh.dwhite.mgz (the outputs of mris_volmmask after binarize them) and the right and left hemispheric white matter masks from aseg.mgz atlas (the output of mri_binarize command line)? I am asking this question because those masks gave me different estimation for the volume? Thanks! Mohamad ___ 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 -- 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] permission denied
Yes, please try running as root and get back when you have the chance. This is a very odd issue and your results when running as root will provide insight. -Zeke Hi Z K, Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one installed with the latest freesurfer version did not work while others finished the processing in a reasonable processing time and I got the results. Also, I have a PC at my office installed with the latest freesurfer version and it works fine. So I have two PCs installed with the latest Freesurfer (one of them which does not work is in the lab). To summarize: All PCs (16 PCs in the lab and 1 in my office) are installed with latest Ubuntu version 14.04 64 bits 15 PCs in the lab are installed with freesurfer 5.0.0 version 1 PC in the lab is installed with the latest freesurfer version (does not work, permission denied) 1 PC in my office is installed with the latest freesurfer version (works fine) All these PCs have Ubuntu 14.04 64bit installed on them. No, I am not using any vitual machine. Regarding the root user, I will try it on Sunday as I am away for a couple of days. Many thanks for your continuous support. Ali On Thu, Oct 30, 2014 at 6:34 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Ali, First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are working properly? I am under the impression that versions of freesurfer pre-version 5.3 will not work on newer linux distributions? In regards to your current permision denied issue... What happens if you try and run tkmedit as root user? Also, you not using virtual machine setup are you? -Zeke On 10/30/2014 06:27 AM, Ali Radaideh wrote: It does not work. This is really strange On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: I beleive it should have a lower case X, as in: chmod -R a+x freesurfer/bin -Zeke On 10/28/2014 01:19 AM, Ali Radaideh wrote: Dear Douglas Thanks for your reply. unfortunatey I still get the same error. Here is the terminal output. Is there anything else I can do? freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl imaging@imaging-ThinkCentre-23:~$ tcsh imaging-ThinkCentre-23:~ tkmedit /usr/local/freesurfer/bin/tkmedit: Permission denied. imaging-ThinkCentre-23:~ On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Try chmod -R a+X freesurfer/bin On 10/26/14 1:57 PM, Ali Radaideh wrote: Dear FreeSurfer users, I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I try a command such such as tkmedit i get the following error /usr/local/freesurfer/bin/tkmedit: permission denied. I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer but did not work. Any ideas why is this happening although I have done the same thing to other PCs and they are working fine. âThanks in advance, Aliâ -- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 390 ext.5422, 5355, 5364 Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ ___ 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
Re: [Freesurfer] White matter volume
Hi Bruce, Actually I am totally confused and this is the reason for my question! What is the best and trusted approach in this case? I want to study the relationship between the FA and the right and left hemispheric white matter. I generated the DTI metrics and volume using FSL. I am sure that the calculated white matter volume in FSL is not correct because it is closer to what I am thinking about. in this case can I use and is it valid if I use the volume from the output of Freesurfer and the metrics from FSL in my analsysis? Thanks From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 11:35 AM To: Freesurfer support list Subject: Re: [Freesurfer] White matter volume Hi Mohamad this is probably due to the partial-volume correction that we typically compute when we estimate volumes in the stats files. cheers Bruce On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote: Thanks Doug, In order to improve my understanding for the analysis that I am working on and in the process of my learning I am tring to calculate the volume in many different ways. Actually It is very easy, simple and possible to use the numbers mentioned in aseg.stats but what if we got different results when we use different methods? I caclated the right and left hemispheric white matter volume in FSL using a mask deriverd from the T1 segmentation in Freesurfer lh.dwhite.mgz , rh.dwhite.mgz then I binarized those masks and I registered them to my T1 then I used the command line fslstats T1 -k my mask -V What surprised me is that the volume was totally different from the one mentioned in aseg.stats (attached) I highly appreciate any advice. looking forward to learn from you Mohamad From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 11:04 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter volume I would suggest using the value in aseg.stats. Is that not possible? On 10/31/2014 10:06 AM, Alshikho, Mohamad J. wrote: Thanks Doug! So do you suggest to use lh.dwhite.mgz , rh.dwhite.mgz the output of mris_volmask? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 10:02 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter volume The aseg is not surface-based and will not be as accurate doug On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote: Hi Bruce, I wanted to calculate the right and left hemispheric white matter volume using a mask. Is there any difference between lh.dwhite.mgz , rh.dwhite.mgz (the outputs of mris_volmmask after binarize them) and the right and left hemispheric white matter masks from aseg.mgz atlas (the output of mri_binarize command line)? I am asking this question because those masks gave me different estimation for the volume? Thanks! Mohamad ___ 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 -- 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] White matter volume
yes. Partial volume correction helps both accuracy and repeatability. You can certainly use our (partial-volume) corrected WM volumes and the FA from FSL if you want cheers Bruce On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote: Hi Bruce, Actually I am totally confused and this is the reason for my question! What is the best and trusted approach in this case? I want to study the relationship between the FA and the right and left hemispheric white matter. I generated the DTI metrics and volume using FSL. I am sure that the calculated white matter volume in FSL is not correct because it is closer to what I am thinking about. in this case can I use and is it valid if I use the volume from the output of Freesurfer and the metrics from FSL in my analsysis? Thanks From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 11:35 AM To: Freesurfer support list Subject: Re: [Freesurfer] White matter volume Hi Mohamad this is probably due to the partial-volume correction that we typically compute when we estimate volumes in the stats files. cheers Bruce On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote: Thanks Doug, In order to improve my understanding for the analysis that I am working on and in the process of my learning I am tring to calculate the volume in many different ways. Actually It is very easy, simple and possible to use the numbers mentioned in aseg.stats but what if we got different results when we use different methods? I caclated the right and left hemispheric white matter volume in FSL using a mask deriverd from the T1 segmentation in Freesurfer lh.dwhite.mgz , rh.dwhite.mgz then I binarized those masks and I registered them to my T1 then I used the command line fslstats T1 -k my mask -V What surprised me is that the volume was totally different from the one mentioned in aseg.stats (attached) I highly appreciate any advice. looking forward to learn from you Mohamad From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 11:04 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter volume I would suggest using the value in aseg.stats. Is that not possible? On 10/31/2014 10:06 AM, Alshikho, Mohamad J. wrote: Thanks Doug! So do you suggest to use lh.dwhite.mgz , rh.dwhite.mgz the output of mris_volmask? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 10:02 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter volume The aseg is not surface-based and will not be as accurate doug On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote: Hi Bruce, I wanted to calculate the right and left hemispheric white matter volume using a mask. Is there any difference between lh.dwhite.mgz , rh.dwhite.mgz (the outputs of mris_volmmask after binarize them) and the right and left hemispheric white matter masks from aseg.mgz atlas (the output of mri_binarize command line)? I am asking this question because those masks gave me different estimation for the volume? Thanks! Mohamad ___ 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 -- 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
Re: [Freesurfer] White matter volume
Thanks a lot!! From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 11:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] White matter volume yes. Partial volume correction helps both accuracy and repeatability. You can certainly use our (partial-volume) corrected WM volumes and the FA from FSL if you want cheers Bruce On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote: Hi Bruce, Actually I am totally confused and this is the reason for my question! What is the best and trusted approach in this case? I want to study the relationship between the FA and the right and left hemispheric white matter. I generated the DTI metrics and volume using FSL. I am sure that the calculated white matter volume in FSL is not correct because it is closer to what I am thinking about. in this case can I use and is it valid if I use the volume from the output of Freesurfer and the metrics from FSL in my analsysis? Thanks From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 11:35 AM To: Freesurfer support list Subject: Re: [Freesurfer] White matter volume Hi Mohamad this is probably due to the partial-volume correction that we typically compute when we estimate volumes in the stats files. cheers Bruce On Fri, 31 Oct 2014, Alshikho, Mohamad J. wrote: Thanks Doug, In order to improve my understanding for the analysis that I am working on and in the process of my learning I am tring to calculate the volume in many different ways. Actually It is very easy, simple and possible to use the numbers mentioned in aseg.stats but what if we got different results when we use different methods? I caclated the right and left hemispheric white matter volume in FSL using a mask deriverd from the T1 segmentation in Freesurfer lh.dwhite.mgz , rh.dwhite.mgz then I binarized those masks and I registered them to my T1 then I used the command line fslstats T1 -k my mask -V What surprised me is that the volume was totally different from the one mentioned in aseg.stats (attached) I highly appreciate any advice. looking forward to learn from you Mohamad From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 11:04 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter volume I would suggest using the value in aseg.stats. Is that not possible? On 10/31/2014 10:06 AM, Alshikho, Mohamad J. wrote: Thanks Doug! So do you suggest to use lh.dwhite.mgz , rh.dwhite.mgz the output of mris_volmask? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, October 31, 2014 10:02 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter volume The aseg is not surface-based and will not be as accurate doug On 10/31/2014 09:14 AM, Alshikho, Mohamad J. wrote: Hi Bruce, I wanted to calculate the right and left hemispheric white matter volume using a mask. Is there any difference between lh.dwhite.mgz , rh.dwhite.mgz (the outputs of mris_volmmask after binarize them) and the right and left hemispheric white matter masks from aseg.mgz atlas (the output of mri_binarize command line)? I am asking this question because those masks gave me different estimation for the volume? Thanks! Mohamad ___ 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 -- 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
