Re: [Freesurfer] your mail
Thank you very much! I will try again following your directions and I'll let you know. Best, Pietro 2013/11/19 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu Hi Pietro, I think you should try redoing the control points from scratch, but with fewer control points and sparser placement. Currently you have 198 control points tightly packed in only a couple regions. Furthermore, there is one control point at 128, 128, 128 which is right in the thalamus which should not be there, maybe an accidental click? Take a look at the placement of the control points in the snapshots on this tutorial page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ ControlPoints_freeview If you compare the norm.mgz volumes before/after editing, you will notice the extreme hyper-intense wm (130+) in the temporal lobes after adding control points and rerunning. The norm.mgz is passed to mri_pretess to create the wm.mgz. You can see there is overlap between the hyper-intense voxels on the norm and the voxels not being included in the wm mask, which leads to major errors in the wm surface. -Louis On Fri, 15 Nov 2013, pietro de rossi wrote: Good morning Dr Vinke, did you have the chance to take a look at the subject I uploaded a few days ago? thanks again. Kind regards, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com 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. -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.comhttp://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli ___ 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] T2pial/FLAIRpial processing issues
Allright; I digged further and further, and finally found out that the sform of our T1 weighted image gets crushed during a lesion filling step earlier in the pipeline. I never recognized this while using FLIRT, maybe because FLIRT uses a different initialization (COG?) than using the header transformation as an initial registration... Anyway, thanks for all the help. It still would be helpfull (I think) to have some kind of QC step in there which could warn if things got wrong. Best, Martijn On Fri, Nov 15, 2013 at 7:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Can you convert the two to mgz or nii with mri_convert and then run tkregister2? If they were acquired in the same session, then the geometric information in the header should bring them into close registration regardless of voxel size, orientation, field of view, etc. mri_convert should preserve this information. dcm2nii should do the same thing, but I did not write it so I don't know what it is doing:). On 11/15/2013 01:15 PM, Martijn Steenwijk wrote: Yes, they were acquired in the same session, but using a slightly different FOV. They were converted from dicom to nifti using dcm2nii and then used for FS analysis. The axis orientation of the images is the same. Extensive image analysis (including registration of FLAIR and T1 using FLIRT) has been run on these images, but I never faced such a problem. Is it possible that left/right orientation is is flipped by FLIRT due to the initial misalignment? On Fri, Nov 15, 2013 at 6:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: were these acquired in the same session? If so, were they converted to mgz directly from dicom? On 11/15/2013 10:15 AM, Martijn Steenwijk wrote: I digged further into this. The scale difference previously reported is not true. It is only a translation error. It looks like that the orig.mgz has (0,0,0) in the center of the image; while FLAIRraw (after header-only registration) has the origin at index (0,0,0) - so in one of the corners of the volume. This means the initial (header based) transformation provided to flirt is also not correct. On Fri, Nov 15, 2013 at 12:49 PM, Martijn Steenwijk martijnsteenw...@gmail.com mailto:martijnsteenw...@gmail.com mailto:martijnsteenw...@gmail.com mailto:martijnsteenw...@gmail.com wrote: Dear all, Thanks for all the input. Doug, concerning your suggestion tkregister2 --mov FLAIRraw.mgz --targ orig.mgz --regheader --reg junk Using this, the axes orientationseem to be correct, but scaling and translation of registered FLAIRraw seem to be way off. (registered FLAIRraw is much larger compared to orig.mgz (in the order of multiple times) and is translated to the radiologically left-caudal part of orig.mgz. mri_convert -rl gives a similar result as using tkregister2 as proposed by Doug. Best, Martijn On Thu, Nov 14, 2013 at 8:38 PM, Douglas N 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: It should not make a difference. We compute an initial registration based on the header and pass that to FLIRT. Can you verify that this initial registration is correct? You can do that with tkregister2 --mov FLAIRraw.mgz --targ orig.mgz --regheader --reg junk If that looks ok, then it is possible that flirt is just failing. Also, newer versions of FS will use an internal version of flirt and so not reliant on FSLDIR being set or FSL being installed. doug On 11/14/2013 12:52 PM, Bruce Fischl wrote: Hi Matt hopefully Doug will chime in, but I don't see why that is the case. We preserve all the RAS information when we conform, so the info should be there for flirt cheers Bruce On Thu, 14 Nov 2013, Matt Glasser wrote: I think you can do it with mri_convert ?rl. I don't think it makes sense to expect FLIRT to get the registration right reliably if the axes are off (in
[Freesurfer] help with save_nifti
Hi,
I am trying to save a nifti file using save_nifti. I'm running into a strange
problem that I describe below.
I have a nifti file (subj_mask.nii) created by a colleague using Nibabel
(http://nipy.sourceforge.net/nibabel/). This volume is in the MNI305 space.
Step1: In a first step I wanted to convert this volume to the fsaverage surface
format. To do that I used :
mri_vol2surf --src subj_mask.nii --hemi rh --out_type mgh --float2int round
--o blah9-rh.mgh --projfrac 0.5 --trgsubject fsaverage --regheader fsaverage.
I load it in tksurfer and when I do view- configure-overlay, I see a range of
values (as expected) and am able to set the min and max thresholds as I want.
Step 2: In a second step I loaded this nifti file into matlab using load_nifti
and had to alter the volume a little bit as below:
hdr=load_nifti('subj_mask.nii');
vol=hdr.vol;
vol(find(vol4))=0;
hdr.vol=vol;
save_nifti(hdr,'new_mask.nii').
I convert the volume to fsaverage surface space as before but when I view it in
tksurfer I am not able to set a min and max threshold with configure-overlay.
Instead, there is no distribution of values plotted in the configure overlay
window and I get the following error message: % ERROR updating histo:
impossible limits (min 0.6 = max 0.6) for axis x
I finally managed to solve this problem by loading the header information from
a FS-FAST created nifti:
hdr_fsfast = load_nifti('bold/analysis.mni/mask.nii.gz');
hdr_fsfast.vol=vol;
save_nifti(hdr_fsfast,'new_mask.nii').
Now I am able to see the distribution of values in the configure overlay window
and am able to set the thresholds.
The headers for FS-FAST and Nibabel generated niftis are indeed slightly
different but why do I not have the problem in step 1 when I use the Nibabel
file, but only in step 2 after I use save_nifti with the Nibabel header ?
I use the load_nifti and save_nifti commands very often (and haven't had
problems before because I was only using FS-FAST generated files) so I would
really appreciate it if someone could point out what is going on so that I
understand what to do in future.
Thanks,
Leila___
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Re: [Freesurfer] hippocampus region in an atlas?
Thank you for the prompt response. You sent exactly what I wanted. Everything worked great! Brian -Original Message- From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu] Sent: Tuesday, November 19, 2013 8:03 AM To: Gregg, Brian E. Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] hippocampus region in an atlas? The entire hippocampus is currently labeled by default in the recon-all stream. You can see it in the aseg.mgz (in the mri directory) and find volume information in stats/aseg.stats. To get the hippocampal subfields you have to run recon-all with an additional flag. This is documented here: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation Allison On Tue, 19 Nov 2013, Gregg, Brian E. wrote: Hello, I didn’t see hippocampus listed in the Desikan-Killiany, Destrieux, or DKTatlas40 atlases. Is there an existing atlas that contains the hippocampal subfields? If not, what options exist for getting the hippocampus into an atlas? Thank you, Brian ___ 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] accessing old releases?
Hello Ruth, That is the correct link. I have accessed the link from multiple networks and I am never prompted for a login and/or password so I am not sure why you would be. Can you try from another network? And just so we are clear, here is the link: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer -Zeke On 11/19/2013 08:19 PM, Ruth Carper wrote: Hi, I need to reinstall an older version of Freesurfer, but the only link I found: Old releases are here. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer seems to require a login and password. How can I access this? ___ 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] Compatibility between RELEASE_I386 i386 and CentOS 6
Dear FS experts,I am forwarding my question (please see below), in case it got lost among the intense flow of messages.Thank you for your consideration.Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 + Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Dear FS experts,I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues.Thank you very much for your attention,Pablo ___ 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] Compatibility between RELEASE_I386 i386 and CentOS 6
Dear Gari,Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6?Thanks,Pablo From: gariko...@gmail.com Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Hi Pablo,you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. PloS one, 7(6), e38234. doi:10.1371/journal.pone.0038234). for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too).regards!Gari On Wed, Nov 20, 2013 at 5:58 PM, pablo najt pablon...@hotmail.com wrote: Dear FS experts,I am forwarding my question (please see below), in case it got lost among the intense flow of messages.Thank you for your consideration.Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 + Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Dear FS experts,I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention,Pablo ___ 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.___ 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] Compatibility between RELEASE_I386 i386 and CentOS 6
I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any reason to not use this version in your CentOS 6, if you have some other requirements maybe Nick or Zeke could help you better, I am just an user :) On Wed, Nov 20, 2013 at 6:47 PM, pablo najt pablon...@hotmail.com wrote: Dear Gari, Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6? Thanks, Pablo -- From: gariko...@gmail.com Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Hi Pablo, you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. *PloS one*, *7*(6), e38234. doi:10.1371/journal.pone.0038234). for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too). regards! Gari On Wed, Nov 20, 2013 at 5:58 PM, pablo najt pablon...@hotmail.com wrote: Dear FS experts, I am forwarding my question (please see below), in case it got lost among the intense flow of messages. Thank you for your consideration. Pablo -- From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 + Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Dear FS experts, I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention, Pablo ___ 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. ___ 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
Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
I have to agree with Gari, I see no reason for you to not use the CentOS6 build. -Zeke On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any reason to not use this version in your CentOS 6, if you have some other requirements maybe Nick or Zeke could help you better, I am just an user :) On Wed, Nov 20, 2013 at 6:47 PM, pablo najt pablon...@hotmail.com mailto:pablon...@hotmail.com wrote: Dear Gari, Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6? Thanks, Pablo From: gariko...@gmail.com mailto:gariko...@gmail.com Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablon...@hotmail.com mailto:pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Hi Pablo, you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. /PloS one/, /7/(6), e38234. doi:10.1371/journal.pone.0038234). for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too). regards! Gari On Wed, Nov 20, 2013 at 5:58 PM, pablo najt pablon...@hotmail.com mailto:pablon...@hotmail.com wrote: Dear FS experts, I am forwarding my question (please see below), in case it got lost among the intense flow of messages. Thank you for your consideration. Pablo From: pablon...@hotmail.com mailto:pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 + Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Dear FS experts, I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention, Pablo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The
Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
Thanks,Pablo Date: Wed, 20 Nov 2013 13:11:15 -0500 From: zkauf...@nmr.mgh.harvard.edu To: gariko...@gmail.com CC: pablon...@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 I have to agree with Gari, I see no reason for you to not use the CentOS6 build. -Zeke On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any reason to not use this version in your CentOS 6, if you have some other requirements maybe Nick or Zeke could help you better, I am just an user :) On Wed, Nov 20, 2013 at 6:47 PM, pablo najt pablon...@hotmail.com mailto:pablon...@hotmail.com wrote: Dear Gari, Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6? Thanks, Pablo From: gariko...@gmail.com mailto:gariko...@gmail.com Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablon...@hotmail.com mailto:pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Hi Pablo, you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. /PloS one/, /7/(6), e38234. doi:10.1371/journal.pone.0038234). for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too). regards! Gari On Wed, Nov 20, 2013 at 5:58 PM, pablo najt pablon...@hotmail.com mailto:pablon...@hotmail.com wrote: Dear FS experts, I am forwarding my question (please see below), in case it got lost among the intense flow of messages. Thank you for your consideration. Pablo From: pablon...@hotmail.com mailto:pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 + Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Dear FS experts, I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention, Pablo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error
[Freesurfer] Bedpost Not successfully completed
Hello, I am finding that my bedposting is not completing successfully. I was able to get my first two subjects to run successfully, however, for the other two subjects that I have run I have gotten the following message: For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /opt/psych_imaging/Freesurfer_5.3//bin/bedpostx_mgh: line 345: kill: (30896) - No such process Any ideas of what I should be looking for or troubleshooting to get this step to work? Thanks so much, Emily ___ 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] recon-all -s subjects -all unexpected termination
Dear all, I have run recon-all for some subjects,but this code is unexpected terminated before it normally end. Can I run the code agian directly without deleting some outputs obtained from recon-all? That is to say, part of recon-all outputs do exist(as I have run recon-all previously), then recon-all new output will overwrite the existing files when I run recon-all again? All the best. 2013-11-21 Rujing Zha___ 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.
