[Freesurfer] ELF class
Hi Fs Team, I am getting this errow while trying to use freeview. reesurfer@freesurfer-VirtualBox:~$ freeview freeview.bin: error while loading shared libraries: libjpeg.so.62: wrong ELF class: ELFCLASS32 Any Help Tx chikku ___ 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 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.
Re: [Freesurfer] make a volume template from the surface-based template for non-human primates
yes, I have it On Tue, 19 Mar 2013, Longchuan Li wrote: Hi, Bruce The command line I used is: mris_fill -r 1 -c rh.white rh.white.nii.gz I attached the rh.white in my previous mail. Could you see it in the attachment? Thank you! Longchuan _ From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, March 19, 2013 8:10 PM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates can you send your mris_fill command line? And maybe the lh.white surface you are trying to fill? Bruce On Tue, 19 Mar 2013, Longchuan Li wrote: Hi, Bruce This is the lh.white that gives me the empty volume when I use mris_fill to sample it to the volume space. Could you help diagnose what is causing it? Thank you very much in advance! Lognchuan From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, March 17, 2013 11:47 AM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates Hi Longchuan I'm not sure what space the volume average is constructed in - Doug would know. Probably talairach, in which case it won't match the surfaces well. Can you send along your mris_fill command line? It shouldn't produce an empty volume. There's no reason to look at the inflated surfaces in the volume though - they have no volumetric meaning. cheers Bruce On Fri, 15 Mar 2013, Longchuan Li wrote: Hi, Bruce Sorry for the late reply as I was trying to figure it out by myself. I mean the average of the subjects in the volume space that were used for generating the surface template. Actually I kind of found a volume average in the mri folder named as T1.mgz that seems to correspond to the surface template for the non-human primates. Perhaps because my ?h.white and ?.pial surface files do not have the identical origins as that of the volume template, when I used the function mri_surf2vol to project the mgh surface file to the volume average, I always got the outputs telling me there is 0 hits. I tried to diagnose it by projecting the ?h.white and ?h.pial to the volume using mri_fill and I got an empty volume. I then tried to project ?h.inflated to the volume space using the mri_fill and this time, I got a mask in the output volume space. Therefore, i suspect that there is a mismatch of the origins between the ?h.white and the volume template in the mri folder. Could you please show me what are the best strategies to correctly project the mgh file to the volume template in the 'mri' folder? Many thanks Longchuan ___ _ From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Longchuan Li leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, March 15, 2013 4:56 PM Subject: Re: [Freesurfer] make a volume template from the surface-based template for non-human primates Hi Longchuan what kind of volume template do you mean? Bruce On Fri, 15 Mar 2013, Longchuan Li wrote: Hi, FreeSurfer experts I have a question regarding making a volume template based on the surface template for non-human primates. I have made a surface template using a group of monkeys and now, we want to see the result, which is a mgh surface file, on the coronal slices of the template. So I am planning to generate a volume template corresponding to the surface template and then project the mgh file to the volume for viewing. Could someone tell me what is the best way to generate such a volume template? Many thanks in advance! Longchuan 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
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.
[Freesurfer] TRACULA missings tracts
Dear Freesurfer users and experts, we have some problems using TRACULA. This means that tracks are missing or that they are too short. I hope you can advise me how to fix these problems. Thanks and kind regards Benjamin ___ 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] Reposting: interpreting clusters from 2 and 3 way interactions
Hi, I wanted to re-post my questions from a couple of days ago below, but with some more specific questions following a search through the archives. I want to be able to extract the beta values from a cluster identified using mc-z in a group by behavioral variable interaction so that I can 1) plot the relationship of thickness to behavioral variable data by group in that cluster, 2) conduct post hoc tests to examine the interaction, and 3) calculate the Rsquare and partial correlations for each variable in the glm (i.e. how much variation in thickness is explained by my behavioral variable). To extract the beta values from a cluster identified by mc-z would I treat the cluster like a label and use mri_segstats to extract the beta weights from the cluster? Would I need to make a label of all the clusters that I want to do this for first? Is there a way to calculate the basic statistics for the glm and extract in table form? i.e. Fs and ps for peaks of each cluster? What about Rsquare, or the correlation between thickness and my behavioral variable in the clusters? or would I need to compute these outside of freesurfer using the extracted betas? Thank you! Laura. On Mon, Mar 18, 2013 at 5:05 PM, Laura M. Tully tully.la...@googlemail.comwrote: Hi Freesurfer experts, I'm hoping you can help me understand how to interpret interactions in clusters identified in whole brain analysis using glmfit and glmfit-sim. Below I describe what I've done and what I'd like to be able to do. Any suggestions would be most appreciated! - I have two groups (patients, controls) and a behavioral variable of interest (social functioning). I am interested in cortical thickness differences between groups (main effect of group), whether cortical thickness relate to social functioning across the group (main effect of social functioning), and whether this relationship differs by group (group x social functioning interaction). - I ran whole brain analysis using mri_glmfit with group and functioning as variables of interest whilst controlling for/regressing out gender, age, and mean thickness. i.e. 4 classes (conmale,confemale, ptmale, ptfemale) and 3 continuous variables (age, AvgThickness, Functioning) = 16 regressors. - I tested the group x functioning interaction with the following contrast - is it correct? 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 - I then ran mri_glmfit-sim to identify clusters that survive multiple comparisons. This revealed 4 clusters (3 in LH; 1 in RH) that represent regions showing significant group x functioning interaction. - I visualized the clusters in tksurfer, and by loading the y.fsgd file was able to visualize the plotted data to get a sense of the interaction, but this is as much as I know in terms of how to examine interactions in the cluster data.. My specifc questions include: - I understand that the values in xxx.sig.cluster.mgh overlay reflect log10 p values, the signs of which indicate the direction of the relationship (i.e. -3 = negative correlation between thickness variable) but I'm not sure how to interpret this in the context of an interaction with group? - I understand that the values in xxx.y.ocn.dat contain the average thickness value for each subject in that cluster and that in a simple between groups test this data could be used to conduct post hoc t-tests to show the direction of the difference, but again I'm not sure how to use this data in the context of the interaction. What do the values represent in a group x variable interaction? Ideally, I'd like to extract the contrast estimates for each subject in the group x functioning contrast and plot it in another program and conduct pairwise comparisons (t-tests) in order to get a better understanding of the interaction). I'm not sure how to do this - is it possible? My thinking is that I do something similar in fMRI analysis in spm where I can plot the contrasts in a significant cluster and then extract both the average contrast estimates for each group and the contrast estimates for each individual subject. Thanks in advance! Laura. -- -- Laura M. Tully, MA Social Neuroscience Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltu...@mednet.ucla.edu ltu...@fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura -- -- Laura M. Tully, MA Social Neuroscience Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltu...@mednet.ucla.edu ltu...@fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura
[Freesurfer] Problem with tracula: incomplete or lacking tracts
Hi list and Anastasia, if you remember the last week I had same problems with tracula output: the final tract are lacking or incomplete for same subjects. Some of these are less wrong (only forceps major), other have more evident error (you can see this in picture that I have attacked). To resolve this issue I have: 1-checked the correct overlap of dwi and dwi_mask2-rerun data with new version 5.23-rerun new registration using bbregister (fsl/spm option): for example, in the subject of the picture attacked, the .mincost file now contains as first value 0.87 (previous it was 1.1) Please, give me an advise Thanks Stefano Messaggio originaleDa: stdp82@virgilio.itData: 12-mar-2013 17.47A: ayend...@nmr.mgh.harvard.eduCc: freesurfer@nmr.mgh.harvard.eduOgg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlapI got it from mri directory but I'm understanding that this directory isn't ok.I'm attacking the image from dlabel/diff/aparc+aseg.bbr.nii Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 12-mar-2013 17.19 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Question on tracula and dwi-T1 overlap Can you please answer my question? I can't really tell if the issue is due poor dwi-aseg overlap unless you tell me where you got that aseg volume from. On Tue, 12 Mar 2013, std...@virgilio.it wrote: Thank you Anastasia. What do you think about the issue in the file attacked (I'm noting that same subjects are lacking of same tracts or same tracts are incomplete) Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 12-mar-2013 17.02 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in the dlabel/diff/ directory has been mapped to the same space as the DWI, so those are the volumes that can be compared directly to dwi.nii.gz. a.y On Tue, 12 Mar 2013, std...@virgilio.it wrote: Hi list, I have two questions, please. I'm using version 5.1 to complete my analysis. 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same subject (figure 1 and 3). You can note the dwi do not overlap to the aseg. How can I resolve this issue? 2-After TRACULA analysis, I'm noting that same subjects are lacking of same tracts or same tracts are incomplete (figure 3). Could it depends from the issue in question 1? I'm thinking to rerun all using version 5.2 but before starting new analyses, I'd like to ask you which is the possible error. Stefano ___ 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] Reposting: interpreting clusters from 2 and 3 way interactions
On 03/20/2013 10:17 AM, Laura M. Tully wrote: Hi, I wanted to re-post my questions from a couple of days ago below, but with some more specific questions following a search through the archives. I want to be able to extract the beta values from a cluster identified using mc-z in a group by behavioral variable interaction so that I can 1) plot the relationship of thickness to behavioral variable data by group in that cluster, 2) conduct post hoc tests to examine the interaction, and 3) calculate the Rsquare and partial correlations for each variable in the glm (i.e. how much variation in thickness is explained by my behavioral variable). To extract the beta values from a cluster identified by mc-z would I treat the cluster like a label and use mri_segstats to extract the beta weights from the cluster? Would I need to make a label of all the clusters that I want to do this for first? You can do it label by label. Or, if the annotation created by mri_glmfit-sim has all the clusters you want, you can use that (also in mri_segstats). You can also create an annotation from individual labels with mris_label2annot. Is there a way to calculate the basic statistics for the glm and extract in table form? i.e. Fs and ps for peaks of each cluster? What about Rsquare, or the correlation between thickness and my behavioral variable in the clusters? or would I need to compute these outside of freesurfer using the extracted betas? You will need to do it outside of FS. What are Fs and ps? doug Thank you! Laura. On Mon, Mar 18, 2013 at 5:05 PM, Laura M. Tully tully.la...@googlemail.com mailto:tully.la...@googlemail.com wrote: Hi Freesurfer experts, I'm hoping you can help me understand how to interpret interactions in clusters identified in whole brain analysis using glmfit and glmfit-sim. Below I describe what I've done and what I'd like to be able to do. Any suggestions would be most appreciated! * I have two groups (patients, controls) and a behavioral variable of interest (social functioning). I am interested in cortical thickness differences between groups (main effect of group), whether cortical thickness relate to social functioning across the group (main effect of social functioning), and whether this relationship differs by group (group x social functioning interaction). * I ran whole brain analysis using mri_glmfit with group and functioning as variables of interest whilst controlling for/regressing out gender, age, and mean thickness. i.e. 4 classes (conmale,confemale, ptmale, ptfemale) and 3 continuous variables (age, AvgThickness, Functioning) = 16 regressors. * I tested the group x functioning interaction with the following contrast - is it correct? 0.50.5-0.5-0.5 * I then ran mri_glmfit-sim to identify clusters that survive multiple comparisons. This revealed 4 clusters (3 in LH; 1 in RH) that represent regions showing significant group x functioning interaction. * I visualized the clusters in tksurfer, and by loading the y.fsgd file was able to visualize the plotted data to get a sense of the interaction, but this is as much as I know in terms of how to examine interactions in the cluster data.. My specifc questions include: * I understand that the values in xxx.sig.cluster.mgh overlay reflect log10 p values, the signs of which indicate the direction of the relationship (i.e. -3 = negative correlation between thickness variable) but I'm not sure how to interpret this in the context of an interaction with group? * I understand that the values in xxx.y.ocn.dat contain the average thickness value for each subject in that cluster and that in a simple between groups test this data could be used to conduct post hoc t-tests to show the direction of the difference, but again I'm not sure how to use this data in the context of the interaction. What do the values represent in a group x variable interaction? Ideally, I'd like to extract the contrast estimates for each subject in the group x functioning contrast and plot it in another program and conduct pairwise comparisons (t-tests) in order to get a better understanding of the interaction). I'm not sure how to do this - is it possible? My thinking is that I do something similar in fMRI analysis in spm where I can plot the contrasts in a significant cluster and then extract both the average contrast estimates for each group and the contrast estimates for each individual subject. Thanks in advance! Laura. -- -- Laura M. Tully, MA Social Neuroscience Psychopathology, Harvard University
Re: [Freesurfer] TRACULA missings tracts
Hi Benjamin - Have you checked that your gradient table is correct by looking at the output of the tensor fit? a.y On Wed, 20 Mar 2013, Roschinski, Benjamin wrote: Dear Freesurfer users and experts, we have some problems using TRACULA. This means that tracks are missing or that they are too short. I hope you can advise me how to fix these problems. Thanks and kind regards Benjamin ___ 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] Problem with tracula: incomplete or lacking tracts
Hi Stefano - Have you checked that your gradient table is correct by looking at the output of the tensor fit? a.y On Wed, 20 Mar 2013, std...@virgilio.it wrote: Hi list and Anastasia, if you remember the last week I had same problems with tracula output: the final tract are lacking or incomplete for same subjects. Some of these are less wrong (only forceps major), other have more evident error (you can see this in picture that I have attacked). To resolve this issue I have: 1-checked the correct overlap of dwi and dwi_mask 2-rerun data with new version 5.2 3-rerun new registration using bbregister (fsl/spm option): for example, in the subject of the picture attacked, the .mincost file now contains as first value 0.87 (previous it was 1.1) Please, give me an advise Thanks Stefano Messaggio originale Da: std...@virgilio.it Data: 12-mar-2013 17.47 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap I got it from mri directory but I'm understanding that this directory isn't ok.I'm attacking the image from dlabel/diff/aparc+aseg.bbr.nii Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 12-mar-2013 17.19 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Question on tracula and dwi-T1 overlap Can you please answer my question? I can't really tell if the issue is due poor dwi-aseg overlap unless you tell me where you got that aseg volume from. On Tue, 12 Mar 2013, std...@virgilio.it wrote: Thank you Anastasia. What do you think about the issue in the file attacked (I'm noting that same subjects are lacking of same tracts or same tracts are incomplete) Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 12-mar-2013 17.02 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in the dlabel/diff/ directory has been mapped to the same space as the DWI, so those are the volumes that can be compared directly to dwi.nii.gz. a.y On Tue, 12 Mar 2013, std...@virgilio.it wrote: Hi list, I have two questions, please. I'm using version 5.1 to complete my analysis. 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same subject (figure 1 and 3). You can note the dwi do not overlap to the aseg. How can I resolve this issue? 2-After TRACULA analysis, I'm noting that same subjects are lacking of same tracts or same tracts are incomplete (figure 3). Could it depends from the issue in question 1? I'm thinking to rerun all using version 5.2 but before starting new analyses, I'd like to ask you which is the possible error. Stefano ___ 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] non-parallel version of LME models MATLAB scripts
In running a mass-univariate LME models analysis I keep running into calls to the parallel computing toolbox (parfor, matlabpool, etc…). I was able to comment out these lines in some of the scripts but I've run up to one that is particularly difficult to modify (I am not an expert in MATLAB). The script called lme_mass_fit_Rgw has proven to be too difficult. Would it be possible to get a version of the of the LME models analysis that runs on the base MATLAB program only? It will admittedly take longer but will make the analysis more accessible. Also, I was unable to find the function for_progress which is called along with parfor_progress. Thanks, Francois ___ 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] Reposting: interpreting clusters from 2 and 3 way interactions
Sorry - meant to respond to list. Thanks for the response Doug - I have a few follow up questions I hope you can clarify: - is the xxx.ocn.annot file created by mri_glmfit-sim considered a label by freesurfer? or does it need to be converted to a label before I can use mri_segstats to extract the betas from the cluster(s) in the xxx.ocn.annot? I tried using the following command line to attempt to extract the betas from the cluster annotation file created by mri_glmfit-sim, but received an error: mri_segstats --i beta.mgh --annot fsaverage hemi contrast/xxx.ocn.annot --avgwf avgwf.dat - how does one convert an xxx.ocn.annot file to a label? - If I have run 3 different glms looking at the relationship between thickness and 3 different behavioral variables, and found 1 (or more) cluster in each glm using mri_glmfit-sim can I create 1 annotation/label with all the clusters from the separate glms and then extract the betas from that one annotation using mri_segstats? Or do I need to treat each glm separately? - I saw on the listserv some references to matlab functions that can calculate r square and partial correlations for glms with more than one predictor variable (e.g pcc between thickness and behavioral variable 1; pcc between thickness and behavioral variable2; Rsq for overall model) but I could not find the .m scripts for the functions (MRIread or fast_glm_pcc?) - would these functions be appropriate and if so where might I find them? Thanks in advance for your help! Laura. On Wed, Mar 20, 2013 at 8:29 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 03/20/2013 10:17 AM, Laura M. Tully wrote: Hi, I wanted to re-post my questions from a couple of days ago below, but with some more specific questions following a search through the archives. I want to be able to extract the beta values from a cluster identified using mc-z in a group by behavioral variable interaction so that I can 1) plot the relationship of thickness to behavioral variable data by group in that cluster, 2) conduct post hoc tests to examine the interaction, and 3) calculate the Rsquare and partial correlations for each variable in the glm (i.e. how much variation in thickness is explained by my behavioral variable). To extract the beta values from a cluster identified by mc-z would I treat the cluster like a label and use mri_segstats to extract the beta weights from the cluster? Would I need to make a label of all the clusters that I want to do this for first? You can do it label by label. Or, if the annotation created by mri_glmfit-sim has all the clusters you want, you can use that (also in mri_segstats). You can also create an annotation from individual labels with mris_label2annot. Is there a way to calculate the basic statistics for the glm and extract in table form? i.e. Fs and ps for peaks of each cluster? What about Rsquare, or the correlation between thickness and my behavioral variable in the clusters? or would I need to compute these outside of freesurfer using the extracted betas? You will need to do it outside of FS. What are Fs and ps? doug Thank you! Laura. On Mon, Mar 18, 2013 at 5:05 PM, Laura M. Tully tully.la...@googlemail.com mailto:tully.la...@googlemail.com wrote: Hi Freesurfer experts, I'm hoping you can help me understand how to interpret interactions in clusters identified in whole brain analysis using glmfit and glmfit-sim. Below I describe what I've done and what I'd like to be able to do. Any suggestions would be most appreciated! * I have two groups (patients, controls) and a behavioral variable of interest (social functioning). I am interested in cortical thickness differences between groups (main effect of group), whether cortical thickness relate to social functioning across the group (main effect of social functioning), and whether this relationship differs by group (group x social functioning interaction). * I ran whole brain analysis using mri_glmfit with group and functioning as variables of interest whilst controlling for/regressing out gender, age, and mean thickness. i.e. 4 classes (conmale,confemale, ptmale, ptfemale) and 3 continuous variables (age, AvgThickness, Functioning) = 16 regressors. * I tested the group x functioning interaction with the following contrast - is it correct? 0.50.5-0.5-0.5 * I then ran mri_glmfit-sim to identify clusters that survive multiple comparisons. This revealed 4 clusters (3 in LH; 1 in RH) that represent regions showing significant group x functioning interaction. * I visualized the clusters in tksurfer, and by loading the y.fsgd
Re: [Freesurfer] Reposting: interpreting clusters from 2 and 3 way interactions
On 03/20/2013 12:09 PM, Laura M. Tully wrote: Sorry - meant to respond to list. Thanks for the response Doug - I have a few follow up questions I hope you can clarify: * is the xxx.ocn.annot file created by mri_glmfit-sim considered a label by freesurfer? It is an annotation * or does it need to be converted to a label before I can use mri_segstats to extract the betas from the cluster(s) in the xxx.ocn.annot? No * I tried using the following command line to attempt to extract the betas from the cluster annotation file created by mri_glmfit-sim, but received an error: mri_segstats --i beta.mgh --annot fsaverage hemi contrast/xxx.ocn.annot --avgwf avgwf.dat That looks correct. Did it work? Add --excludeid 0 to keep it from reporting on non-clusters * how does one convert an xxx.ocn.annot file to a label? If needed, use mri_annotation2label * If I have run 3 different glms looking at the relationship between thickness and 3 different behavioral variables, and found 1 (or more) cluster in each glm using mri_glmfit-sim can I create 1 annotation/label with all the clusters from the separate glms and then extract the betas from that one annotation using mri_segstats? Or do I need to treat each glm separately? It is probably easiest if you treat each glm separately. You can break the annotations into separate labels, then recombine the labels into another annotation (mris_label2annot), but it is a lot of work. * * I saw on the listserv some references to matlab functions that can calculate r square and partial correlations for glms with more than one predictor variable (e.g pcc between thickness and behavioral variable 1; pcc between thickness and behavioral variable2; Rsq for overall model) but I could not find the .m scripts for the functions (MRIread or fast_glm_pcc?) - would these functions be appropriate and if so where might I find them? Yes. They are in $FREESURFER_HOME/matlab and $FREESURFER_HOME/fsfast/toolbox doug * Thanks in advance for your help! Laura. On Wed, Mar 20, 2013 at 8:29 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 03/20/2013 10:17 AM, Laura M. Tully wrote: Hi, I wanted to re-post my questions from a couple of days ago below, but with some more specific questions following a search through the archives. I want to be able to extract the beta values from a cluster identified using mc-z in a group by behavioral variable interaction so that I can 1) plot the relationship of thickness to behavioral variable data by group in that cluster, 2) conduct post hoc tests to examine the interaction, and 3) calculate the Rsquare and partial correlations for each variable in the glm (i.e. how much variation in thickness is explained by my behavioral variable). To extract the beta values from a cluster identified by mc-z would I treat the cluster like a label and use mri_segstats to extract the beta weights from the cluster? Would I need to make a label of all the clusters that I want to do this for first? You can do it label by label. Or, if the annotation created by mri_glmfit-sim has all the clusters you want, you can use that (also in mri_segstats). You can also create an annotation from individual labels with mris_label2annot. Is there a way to calculate the basic statistics for the glm and extract in table form? i.e. Fs and ps for peaks of each cluster? What about Rsquare, or the correlation between thickness and my behavioral variable in the clusters? or would I need to compute these outside of freesurfer using the extracted betas? You will need to do it outside of FS. What are Fs and ps? doug Thank you! Laura. On Mon, Mar 18, 2013 at 5:05 PM, Laura M. Tully tully.la...@googlemail.com mailto:tully.la...@googlemail.com mailto:tully.la...@googlemail.com mailto:tully.la...@googlemail.com wrote: Hi Freesurfer experts, I'm hoping you can help me understand how to interpret interactions in clusters identified in whole brain analysis using glmfit and glmfit-sim. Below I describe what I've done and what I'd like to be
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.
Re: [Freesurfer] Reposting: interpreting clusters from 2 and 3 way interactions
the mri_segstats command did not work - below is the command and output. It looks like it is searching for the .annot file in fsaverage directory. How do I tell it to use fsaverage and to look for the .annot elsewhere? cd glmdir mri_segstats --i beta.mgh --annot fsaverage lh ./SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot --avgwf lh.SZ_CPT_area_betas.dat --excludeid 0 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --i beta.mgh --annot fsaverage lh ./SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot --avgwf lh.SZ_CPT_area_betas.dat --excludeid 0 sysname Linux hostname ncfws12.rc.fas.harvard.edu machine x86_64 user ltully Constructing seg from annotation could not read annot file /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh../SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot.annot No such file or directory Thanks! LT On Wed, Mar 20, 2013 at 9:54 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: On 03/20/2013 12:09 PM, Laura M. Tully wrote: Sorry - meant to respond to list. Thanks for the response Doug - I have a few follow up questions I hope you can clarify: * is the xxx.ocn.annot file created by mri_glmfit-sim considered a label by freesurfer? It is an annotation * or does it need to be converted to a label before I can use mri_segstats to extract the betas from the cluster(s) in the xxx.ocn.annot? No * I tried using the following command line to attempt to extract the betas from the cluster annotation file created by mri_glmfit-sim, but received an error: mri_segstats --i beta.mgh --annot fsaverage hemi contrast/xxx.ocn.annot --avgwf avgwf.dat That looks correct. Did it work? Add --excludeid 0 to keep it from reporting on non-clusters * how does one convert an xxx.ocn.annot file to a label? If needed, use mri_annotation2label * If I have run 3 different glms looking at the relationship between thickness and 3 different behavioral variables, and found 1 (or more) cluster in each glm using mri_glmfit-sim can I create 1 annotation/label with all the clusters from the separate glms and then extract the betas from that one annotation using mri_segstats? Or do I need to treat each glm separately? It is probably easiest if you treat each glm separately. You can break the annotations into separate labels, then recombine the labels into another annotation (mris_label2annot), but it is a lot of work. * * I saw on the listserv some references to matlab functions that can calculate r square and partial correlations for glms with more than one predictor variable (e.g pcc between thickness and behavioral variable 1; pcc between thickness and behavioral variable2; Rsq for overall model) but I could not find the .m scripts for the functions (MRIread or fast_glm_pcc?) - would these functions be appropriate and if so where might I find them? Yes. They are in $FREESURFER_HOME/matlab and $FREESURFER_HOME/fsfast/** toolbox doug * Thanks in advance for your help! Laura. On Wed, Mar 20, 2013 at 8:29 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: On 03/20/2013 10:17 AM, Laura M. Tully wrote: Hi, I wanted to re-post my questions from a couple of days ago below, but with some more specific questions following a search through the archives. I want to be able to extract the beta values from a cluster identified using mc-z in a group by behavioral variable interaction so that I can 1) plot the relationship of thickness to behavioral variable data by group in that cluster, 2) conduct post hoc tests to examine the interaction, and 3) calculate the Rsquare and partial correlations for each variable in the glm (i.e. how much variation in thickness is explained by my behavioral variable). To extract the beta values from a cluster identified by mc-z would I treat the cluster like a label and use mri_segstats to extract the beta weights from the cluster? Would I need to make a label of all the clusters that I want to do this for first? You can do it label by label. Or, if the annotation created by mri_glmfit-sim has all the clusters you want, you can use that (also in mri_segstats). You can also create an annotation from individual labels with mris_label2annot. Is there a way to calculate the basic statistics for the
[Freesurfer] (no subject)
Hi FreeSurfer experts, I would need to use the registration tools in freesurfer because the fsl ones ga ve me some problem. Just to try I have run mri_ca_registration and mri_cvs_registration and so I hav e three questions: 1) mri_ca_registration generates a talairach tansform file in .m3z format and I would need to apply it to my high res image. Any hint? 2) Converting RB_all_2008-03-26.gca to nii and opening it to mricron it seems to superimposable to the mni atlas. does it mean that what it comes out from mri_c a_registration coincides to an mni atlas image? 3) Running mri_cvs_registration (on bert data...just to try) I do not know where to find the registered volume file (I have tried few volume .mgz but with no su ccess...). Should i look for a transform file too? Thanks so much! Martina ___ 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] Asymmetries of cortical thickness
Hi Sophie, you can run the following command: cd $SUBJECTS_DIR/yoursubject mris_apply_reg --src xhemi/surf/lh.thickness --streg xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg --tval surf/lh.rh.thickness.mgh lh.rh.thickness.mgh will now have the rh thicknesses on the rh surface mris_apply_reg is only available in 5.2. If you don't have 5.2, I can get you a version of this program if you tell me your OS. Also note that you need to go through the xhemi-reg procedure first. doug On 03/18/2013 10:40 AM, Sophie Maingault wrote: Yes if it is possible I would like to know how to do it ? Thanks ! Sophie -Message d'origine- De : Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Envoyé : lundi 18 mars 2013 14:39 À : Sophie Maingault; Freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Asymmetries of cortical thickness It is possible, it is just not a good idea because if you map rh to lh and then compare to lh, the rh will have been interpolated to get it into the lh. Even if there are no differences between the two, you will see differences because of the interpolation. Mapping both to fsaverage_sym means that both will be interpolated. If this interpolation does not bother you, then I can show you how to get it from rh to lh. doug On 03/18/2013 09:24 AM, Sophie Maingault wrote: So i didn't understand what you mean by just specify one subject when your mris_preproc ? Because, in fact I don't want to use the registration on fsaverage_sym. I would like just to create a file lh.thickness less rh.thickness vertex per vertex, maybe it is not possible ? -Message d'origine- De : Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Envoyé : lundi 18 mars 2013 14:15 À : Sophie Maingault; Freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Asymmetries of cortical thickness No, it is not, the target needs to be fsaverage_sym doug On 03/18/2013 09:13 AM, Sophie Maingault wrote: So I do : mris_preproc --target fsaverage --xhemi --hemi lh --paired-diff --meas thickness --out lh.lh-rh.thickness.sm00.mgh --s t0001 --s t0003 --s t0009 --s t0027 --s t0031 --s t0033 --s t0126 --s t0148 --s t0171 --s t0174 --s t0199 --s t0203 --s t0212 --s t0215 --s t0242 --s t0245 --s t0253 --s t0254 --s t0256 --s t0268 You think it's ok ? Sophie -Message d'origine- De : freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Douglas N Greve Envoyé : lundi 18 mars 2013 13:49 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Asymmetries of cortical thickness you will have to use the same stream, just specify one subject when your mris_preproc doug On 03/18/2013 08:06 AM, Sophie Maingault wrote: Hello, Iobtained a map of cortical thickness asymmetries after the registration on the symmetric atlas. But I would to obtain the same map with raw data I mean just by subtract lh.thickness and rh.thickness. How can I modify the part #Create a stack of subjects in wiki page ? I have to register to fsaverage (and not fsaverage_sym) and then do the same thing ? Thanks you for your help. Sophie ___ 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: 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] freeview warning: invalid drawable
Dear freesurfer experts, I'm wondering why I get this warning message when I open up any surf template in either fsaverage or fsaverage_sym directory. FYI, I'm using freeview v1.0 if anybody know, please help. -Glen $ freeview -f lh.inflated 2013-03-20 16:03:05.801 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.805 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.823 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.825 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.844 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.846 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.863 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.865 freeview.bin[52449:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) 2013-03-20 16:03:06.211 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:06.212 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:06.213 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:11.634 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:11.638 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:11.649 freeview.bin[52449:907] invalid drawable ___ 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] freeview warning: invalid drawable
On a Mac? You can just ignore those warning messages. Unfortunately we were unable to remove them. Ruopeng On 03/20/2013 04:07 PM, Glen Lee wrote: Dear freesurfer experts, I'm wondering why I get this warning message when I open up any surf template in either fsaverage or fsaverage_sym directory. FYI, I'm using freeview v1.0 if anybody know, please help. -Glen $ freeview -f lh.inflated 2013-03-20 16:03:05.801 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.805 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.823 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.825 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.844 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.846 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.863 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:05.865 freeview.bin[52449:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) 2013-03-20 16:03:06.211 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:06.212 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:06.213 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:11.634 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:11.638 freeview.bin[52449:907] invalid drawable 2013-03-20 16:03:11.649 freeview.bin[52449:907] invalid drawable ___ 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] Reposting: interpreting clusters from 2 and 3 way interactions
Try using this version of mri_segstats ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats doug On 03/20/2013 01:10 PM, Laura M. Tully wrote: the mri_segstats command did not work - below is the command and output. It looks like it is searching for the .annot file in fsaverage directory. How do I tell it to use fsaverage and to look for the .annot elsewhere? cd glmdir mri_segstats --i beta.mgh --annot fsaverage lh ./SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot --avgwf lh.SZ_CPT_area_betas.dat --excludeid 0 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --i beta.mgh --annot fsaverage lh ./SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot --avgwf lh.SZ_CPT_area_betas.dat --excludeid 0 sysname Linux hostname ncfws12.rc.fas.harvard.edu http://ncfws12.rc.fas.harvard.edu machine x86_64 user ltully Constructing seg from annotation could not read annot file /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh../SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot.annot No such file or directory Thanks! LT On Wed, Mar 20, 2013 at 9:54 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 03/20/2013 12:09 PM, Laura M. Tully wrote: Sorry - meant to respond to list. Thanks for the response Doug - I have a few follow up questions I hope you can clarify: * is the xxx.ocn.annot file created by mri_glmfit-sim considered a label by freesurfer? It is an annotation * or does it need to be converted to a label before I can use mri_segstats to extract the betas from the cluster(s) in the xxx.ocn.annot? No * I tried using the following command line to attempt to extract the betas from the cluster annotation file created by mri_glmfit-sim, but received an error: mri_segstats --i beta.mgh --annot fsaverage hemi contrast/xxx.ocn.annot --avgwf avgwf.dat That looks correct. Did it work? Add --excludeid 0 to keep it from reporting on non-clusters * how does one convert an xxx.ocn.annot file to a label? If needed, use mri_annotation2label * If I have run 3 different glms looking at the relationship between thickness and 3 different behavioral variables, and found 1 (or more) cluster in each glm using mri_glmfit-sim can I create 1 annotation/label with all the clusters from the separate glms and then extract the betas from that one annotation using mri_segstats? Or do I need to treat each glm separately? It is probably easiest if you treat each glm separately. You can break the annotations into separate labels, then recombine the labels into another annotation (mris_label2annot), but it is a lot of work. * * I saw on the listserv some references to matlab functions that can calculate r square and partial correlations for glms with more than one predictor variable (e.g pcc between thickness and behavioral variable 1; pcc between thickness and behavioral variable2; Rsq for overall model) but I could not find the .m scripts for the functions (MRIread or fast_glm_pcc?) - would these functions be appropriate and if so where might I find them? Yes. They are in $FREESURFER_HOME/matlab and $FREESURFER_HOME/fsfast/toolbox doug * Thanks in advance for your help! Laura. On Wed, Mar 20, 2013 at 8:29 AM, 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: On 03/20/2013 10:17 AM, Laura M. Tully wrote: Hi, I wanted to re-post my questions from a couple of days ago below, but with some more specific questions following a search through the archives. I want to be able to extract the beta values from a cluster identified using mc-z in a group by behavioral variable interaction so that I can 1)
[Freesurfer] mri_info crashing (bits stored vs bits allocated?)
We have a data set that mri_info cannot work with. We've tried multiple architectures and freesurfer versions, but mri_info either crashes with segmentation fault or generates errors such as *** glibc detected *** mri_info: free(): invalid pointer: 0x006b *** One feature of the data set is that the bits stored(12) is different than the bits allocated(16). Could this be the problem? I have an anonymized version of the data set I can upload if that helps. Thanks for any assistance, John ___ 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_info crashing (bits stored vs bits allocated?)
Hi John if you email it to me I'll take a look Bruce On Wed, 20 Mar 2013, Ostuni, John (NIH/NINDS) [E] wrote: We have a data set that mri_info cannot work with. We've tried multiple architectures and freesurfer versions, but mri_info either crashes with segmentation fault or generates errors such as *** glibc detected *** mri_info: free(): invalid pointer: 0x006b *** One feature of the data set is that the bits stored(12) is different than the bits allocated(16). Could this be the problem? I have an anonymized version of the data set I can upload if that helps. Thanks for any assistance, John ___ 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] libjpeg.so.62
Hi all, My RA's are having similar issues running Freeview on Ubuntu (I've read others are having the same issue). They get the following error when trying to call freeview: freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory We ran apt-get install libjpeg62 to install missing libraries, and when that didn't fix the issue we tried Nick's fix below just in case it might work. Unfortunately we are still getting the error. Any ideas about what's going on? Thank you in advance for your assistance! On Tue, Feb 26, 2013 at 7:47 AM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: Chikku, I am guessing that you are using Ubuntu. To fix this problem: cd /usr/lib sudo ln -s libjpeg.so.8 libjpeg.so.62 in other words, link whatever libjpeg is already installed to the name libjpeg.so.62. Nick Hi I am getting an error while using qdec. It says error while loading shared libraries ,libjpeg.so.62 cannot open shared object file No such file or directory I ran reconall with out any problem. Any idea, tx chikku ___ 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. -- Ashley A. Shurick Graduate Student, Psychology Stanford University ___ 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] y values from glmfit-sim
Hello experts, could someone clarify for me what the y values in the xxx.ocn.y.dat files represent following glmfit-sim? are they the residualized y values of avg cortical thickness in that specific cluster after regressing out the effect of any predictor variables in the glm? Thanks! Laura. -- -- Laura M. Tully, MA Social Neuroscience Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltu...@mednet.ucla.edu ltu...@fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura ___ 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_info crashing (bits stored vs bits allocated?)
HI I have similar problem and filled a bug report at. Product: Fedorahttps://bugzilla.redhat.com/show_bug.cgi?id=905638 Patsy Franklinpfran...@redhat.com changed: What |Removed |Added Flags|needinfo?(pfrankli@redhat.c | |om) | Flags|needinfo?(pfrankli@redhat.c | |om) | --- Comment #27 from Patsy Franklinpfran...@redhat.com --- The most immediate solution is for the application to be changed to use a compliant crypt salt value. After further investigation, we found that the application is passing unsupported, nonstandard salt to crypt(). This will result in crypt() returning NULL and setting errno to EINVAL. It does not appear that the application is checking for a NULL return value from crypt. It also appears that the application is using this NULL return value in a subsequent function call resulting in a segmentation fault. Previously glibc would accept unsupported salt values, but newer versions of the library have become stricter. We are currently reviewing the implementation to see if the accepted salt values can be expanded while still meeting our standards compliance requirements. -- Knut J On 03/20/2013 09:59 PM, Bruce Fischl wrote: Hi John if you email it to me I'll take a look Bruce On Wed, 20 Mar 2013, Ostuni, John (NIH/NINDS) [E] wrote: We have a data set that mri_info cannot work with. We've tried multiple architectures and freesurfer versions, but mri_info either crashes with segmentation fault or generates errors such as *** glibc detected *** mri_info: free(): invalid pointer: 0x006b *** One feature of the data set is that the bits stored(12) is different than the bits allocated(16). Could this be the problem? I have an anonymized version of the data set I can upload if that helps. Thanks for any assistance, John ___ 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
[Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts
Thank you Anastasia. I'm checking gradient table but I would like underline that I'm noting some holes in dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative images). Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 16.40 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts Hi Stefano - Have you checked that your gradient table is correct by looking at the output of the tensor fit? a.y On Wed, 20 Mar 2013, std...@virgilio.it wrote: Hi list and Anastasia, if you remember the last week I had same problems with tracula output: the final tract are lacking or incomplete for same subjects. Some of these are less wrong (only forceps major), other have more evident error (you can see this in picture that I have attacked). To resolve this issue I have: 1-checked the correct overlap of dwi and dwi_mask 2-rerun data with new version 5.2 3-rerun new registration using bbregister (fsl/spm option): for example, in the subject of the picture attacked, the .mincost file now contains as first value 0.87 (previous it was 1.1) Please, give me an advise Thanks Stefano Messaggio originale Da: std...@virgilio.it Data: 12-mar-2013 17.47 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap I got it from mri directory but I'm understanding that this directory isn't ok.I'm attacking the image from dlabel/diff/aparc+aseg.bbr.nii Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 12-mar-2013 17.19 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Question on tracula and dwi-T1 overlap Can you please answer my question? I can't really tell if the issue is due poor dwi-aseg overlap unless you tell me where you got that aseg volume from. On Tue, 12 Mar 2013, std...@virgilio.it wrote: Thank you Anastasia. What do you think about the issue in the file attacked (I'm noting that same subjects are lacking of same tracts or same tracts are incomplete) Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 12-mar-2013 17.02 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in the dlabel/diff/ directory has been mapped to the same space as the DWI, so those are the volumes that can be compared directly to dwi.nii.gz. a.y On Tue, 12 Mar 2013, std...@virgilio.it wrote: Hi list, I have two questions, please. I'm using version 5.1 to complete my analysis. 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same subject (figure 1 and 3). You can note the dwi do not overlap to the aseg. How can I resolve this issue? 2-After TRACULA analysis, I'm noting that same subjects are lacking of same tracts or same tracts are incomplete (figure 3). Could it depends from the issue in question 1? I'm thinking to rerun all using version 5.2 but before starting new analyses, I'd like to ask you which is the possible error. Stefano ___ 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
Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts
There are chunks of the brain missing from the brain mask. This may cause some tracts to be incomplete or missing. But you should still check that the gradient directions are correct, so you know if you have multiple problems or just one. The FA map can't tell you if the gradient table was correct, you have to check the eigenvectors in dtifit_V1 for that. On Wed, 20 Mar 2013, std...@virgilio.it wrote: File attacked Messaggio originale Da: std...@virgilio.it Data: 20-mar-2013 22.34 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts Thank you Anastasia. I'm checking gradient table but I would like underline that I'm noting some holes in dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative images). Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 16.40 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts Hi Stefano - Have you checked that your gradient table is correct by looking at the output of the tensor fit? a.y On Wed, 20 Mar 2013, std...@virgilio.it wrote: Hi list and Anastasia, if you remember the last week I had same problems with tracula output: the final tract are lacking or incomplete for same subjects. Some of these are less wrong (only forceps major), other have more evident error (you can see this in picture that I have attacked). To resolve this issue I have: 1-checked the correct overlap of dwi and dwi_mask 2-rerun data with new version 5.2 3-rerun new registration using bbregister (fsl/spm option): for example, in the subject of the picture attacked, the .mincost file now contains as first value 0.87 (previous it was 1.1) Please, give me an advise Thanks Stefano Messaggio originale Da: std...@virgilio.it Data: 12-mar-2013 17.47 A: ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap I got it from mri directory but I'm understanding that this directory isn't ok.I'm attacking the image from dlabel/diff/aparc+aseg.bbr.nii Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 12-mar-2013 17.19 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Question on tracula and dwi-T1 overlap Can you please answer my question? I can't really tell if the issue is due poor dwi-aseg overlap unless you tell me where you got that aseg volume from. On Tue, 12 Mar 2013, std...@virgilio.it wrote: Thank you Anastasia. What do you think about the issue in the file attacked (I'm noting that same subjects are lacking of same tracts or same tracts are incomplete) Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 12-mar-2013 17.02 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in the dlabel/diff/ directory has been mapped to the same space as the DWI, so those are the volumes that can be compared directly to dwi.nii.gz. a.y On Tue, 12 Mar 2013, std...@virgilio.it wrote: Hi list, I have two questions, please. I'm using version 5.1 to complete my analysis. 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same subject (figure 1 and 3). You can note the dwi do not overlap to the aseg. How can I resolve this issue? 2-After TRACULA analysis, I'm noting that same subjects are lacking of same tracts or same tracts are incomplete (figure 3). Could it depends from the issue in question 1? I'm thinking to rerun all using version 5.2 but before starting new analyses, I'd like to ask you which is the possible error. Stefano ___ 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
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.
[Freesurfer] installation problem
dear freesurfer experts, I tried to install freesurfer in a remote linux cluster, when I completed the installation, and began to run the freesurfer gui use my own windows PC, the command line showed erro belowing information : [wanglhlab@node01 freesurfer]$ tkmedit bert orig.mgz GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: localhost:11.0 could anyone tell me the reason why my installation failed? The video card on cluster is Matrox Graphics, Inc. MGA G200eW WPCM450 (rev 0a), my own PC video card is AMD Radeon HD 7800 Series. regards Xue Zhang___ 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.
