Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer?
On Tue, Aug 16, 2011 at 1:42 PM, Leo Souza lso...@nvidia.com wrote: Does anyone knows how do I run a benchmark test on GPU with FreeSurfer and CUDA? Beyond running a comparison between [x] and [x]_cuda? If you want numbers on individual routines, then the cudatest directory holds a lot of test cases which will run one routine and compare timings (these are used by the tests under test_tm). Could you explain what information you're looking for? Richard ___ 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_glmfit-sim
Dear Doug, Thank you very much for your valuable reply. I still have few questions on which I would like to ask your advise: QUESTION 1: While running the recall-all for all my subjects I also used the -qcache option. I am not sure how this data is further used for my GLM analysis. I will appreciate if you can confirm if in this case in order to do a thickness-age correlation group study I need to complete the following steps: STEP 1: Uncached Data: resamples each subjects data to fsaveragea (into a common space), and Concatenating all the subjects' into a single file by running mris_preproc --fsgd AGE_fsgd.fsgd \ --target fsaverage --hemi lh \ --meas thickness \ --out lh.AGE.thickness.00.mgh STEP 2: The independent variable is the thickness smoothed at various FWHM (full-width/half-max), usually 0, 5, 10, 10, 20, and 25mm so run: mris_preproc --fsgd AGE_fsgd.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.AGE.thickness.10.mgh STEP 3: If I run the next step (I know is optional) where I can use this data lh.AGE.thickness.10B.mgh? Is this a better data to be use for my further steps? OPTIONAL: THIS WILL TAKE ABOUT 5 MINUTES mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.AGE.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.AGE.thickness.10B.mgh STEP 4: GLM Analysis (mri_glmfit) mri_glmfit \ --y lh.AGE.thickness.10.mgh \ --fsgd AGE_fsgd.fsgd dods\ --C lh-Avg-thickness-age-Cor.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.AGE.glmdir STEP 5: View the uncorrected significance map with tksurfer: tksurfer fsaverage lh inflated \ -annot aparc.annot -fthresh 2 \ -overlay lh.AGE.glmdir/lh-Avg-thickness-age-Cor/sig.mgh STEP 6: Viewing the medial surface, change the overlay threshold to something very, very low (say, .01), View -- Configure -- Overlay, set Min .01 STEP 7: CSD (Cluster Simulation Data)- Run the Simulation mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg \ --overwrite QUESTION 2: You mentioned that I should use the --cache option to mri_glmfit-sim. How I should do this? Do I need to change STEP 7? QUESTION 3: How I can check my data to make sure that I have actual activation above the voxel-wise threshold and how I can change my threshold? Based on what I need to change my threshold? Do I change my treshold until I find some activation? Thank you very much for your valuable help. Antonella From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, August 16, 2011 12:04 PM Subject: Re: [Freesurfer] thickness-age correlation Antonella Kis wrote: Dear Freesurfer experts, I am doing a thickness-age correlation group difference study (patients versus controls. I would like to know if: 1) my contrast vector defined as 0 0 0.5 0.5 is correct in order to test the change in thickness with age Yes. 2)what is the best iteration number for the simulation? Should be 5000 or 1000 or greater? 10,000 -- note that if you're doing a whole-hemisphere correction with the monte-carlo simulation then you should use the pre-computed results (use the --cache option to mri_glmfit-sim) 3)why when I run the simulation for 5 iterations I've got zero clusters? You should look at your data to make sure that you have actual activation above the voxel-wise threshold you have set. Also, only 5 clusters would not be enough to get a significant cluster anyway. 4)can I derive the thickness from the significant clusters of glm analysis? Do I need to run QDEC after GLM? If you mean that you want the average thickness from each subject for a given cluster, then this information is generated with mri_glmfit-sim in the csdbase.y.ocn.dat file. doug Thanks for any enlightenment. Antonella ___ 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 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
[Freesurfer] DOSS or DODS
Dear all, I have two groups of subjects, and I want to see a difference in thickness between them controlling for age. I couldn't find any information in the literature on how the subject's brains in my groups develop with age. Therefore I can't tell whether thickness as a function of age for both groups has the same slope or different. My question is if in this case I should use DODS? Thank you, Tanja. ___ 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] DOSS or DODS
Hi Tanja, you should use DODS and test for a difference between the age slopes of the groups (ie, an interaction between group and age). If there are no significant interactions, you should then use DOSS to test for the difference between thicknesses. doug Tetiana Dadakova wrote: Dear all, I have two groups of subjects, and I want to see a difference in thickness between them controlling for age. I couldn't find any information in the literature on how the subject's brains in my groups develop with age. Therefore I can't tell whether thickness as a function of age for both groups has the same slope or different. My question is if in this case I should use DODS? Thank you, Tanja. ___ 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 ___ 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_glmfit-sim
Antonella Kis wrote: Dear Doug, Thank you very much for your valuable reply. I still have few questions on which I would like to ask your advise: QUESTION 1: While running the recall-all for all my subjects I also used the -qcache option. I am not sure how this data is further used for my GLM analysis. I will appreciate if you can confirm if in this case in order to do a thickness-age correlation group study I need to complete the following steps: STEP 1: Uncached Data: resamples each subjects data to fsaveragea (into a common space), and Concatenating all the subjects' into a single file by running mris_preproc --fsgd AGE_fsgd.fsgd \ --target fsaverage --hemi lh \ --meas thickness \ --out lh.AGE.thickness.00.mgh STEP 2: The independent variable is the thickness smoothed at various FWHM (full-width/half-max), usually 0, 5, 10, 10, 20, and 25mm so run: mris_preproc --fsgd AGE_fsgd.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.AGE.thickness.10.mgh STEP 3: If I run the next step (I know is optional) where I can use this data lh.AGE.thickness.10B.mgh? Is this a better data to be use for my further steps? You would use it in the same place that you would use lh.AGE.thickness.10.mgh. It is just a different way to compute it if you did not qcache. OPTIONAL: THIS WILL TAKE ABOUT 5 MINUTES mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.AGE.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.AGE.thickness.10B.mgh STEP 4: GLM Analysis (mri_glmfit) mri_glmfit \ --y lh.AGE.thickness.10.mgh \ --fsgd AGE_fsgd.fsgd dods\ --C lh-Avg-thickness-age-Cor.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.AGE.glmdir STEP 5: View the uncorrected significance map with tksurfer: tksurfer fsaverage lh inflated \ -annot aparc.annot -fthresh 2 \ -overlay lh.AGE.glmdir/lh-Avg-thickness-age-Cor/sig.mgh STEP 6: Viewing the medial surface, change the overlay threshold to something very, very low (say, .01), View -- Configure -- Overlay, set Min .01 STEP 7: CSD (Cluster Simulation Data)- Run the Simulation mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg \ --overwrite QUESTION 2: You mentioned that I should use the --cache option to mri_glmfit-sim. How I should do this? Do I need to change STEP 7? Yes, use mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --cache 4 neg \ --overwrite QUESTION 3: How I can check my data to make sure that I have actual activation above the voxel-wise threshold and how I can change my threshold? Based on what I need to change my threshold? Do I change my treshold until I find some activation? Run tksurfer to view the sig.mgh file. Set the threshold to the one you used in mri_glmfit-sim using the view-configure-overlay. There are no hard and fast rules to setting thresholds, but people usually use p.05 or p.01. doug Thank you very much for your valuable help. Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Tuesday, August 16, 2011 12:04 PM *Subject:* Re: [Freesurfer] thickness-age correlation Antonella Kis wrote: Dear Freesurfer experts, I am doing a thickness-age correlation group difference study (patients versus controls. I would like to know if: 1) my contrast vector defined as 0 0 0.5 0.5 is correct in order to test the change in thickness with age Yes. 2)what is the best iteration number for the simulation? Should be 5000 or 1000 or greater? 10,000 -- note that if you're doing a whole-hemisphere correction with the monte-carlo simulation then you should use the pre-computed results (use the --cache option to mri_glmfit-sim) 3)why when I run the simulation for 5 iterations I've got zero clusters? You should look at your data to make sure that you have actual activation above the voxel-wise threshold you have set. Also, only 5 clusters would not be enough to get a significant cluster anyway. 4)can I derive the thickness from the significant clusters of glm analysis? Do I need to run QDEC after GLM? If you mean that you want the average thickness from each subject for a given cluster, then this information is generated with mri_glmfit-sim in the csdbase.y.ocn.dat file. doug Thanks for any enlightenment. Antonella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Re: [Freesurfer] mri_glmfit-sim
Hi Doug, Thanks again for your help. There are few more things not very clear for me and I will be very graetful if you can advise me: 1). Did you mean that if I did not qcache my data while I was doing pre-processing running the recon-all I should use then lh.AGE.thickness.10B.mgh? 2) Are then the mentioned steps the right one to be followed? 3) I saw on one tutorial about the mri_glm to perform estimations. What are this estimations? Do I need to run: # For the left hemisphere mris_glm --surfmeas thickness \ --hemi lh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100lh.mgz\ --var ./var_doss-thickness-100lh.mgz \ --y ./y_doss-thickness-100lh_000.mgz \ --nsmooth 100 # For the right hemisphere mris_glm --surfmeas thickness \ --hemi rh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100rh.mgz \ --var ./var_doss-thickness-100rh.mgz \ --y ./y_doss-thickness-100rh_000.mgz \ --nsmooth 100 4) If I have less than 80 subjects do I need to run the full MC simulation and I must supply the smoothest of my data as fwhm from the y.fsgd file? Also I would need to mention the threshold like in the following example? mri_glmfit --y lh.gender_age.thickness.10.mgh \ --glmdir lh.gender_age.glmdir \ --fsgd gender_age.txt doss \ --surf fsaverage lh \ --fwhm 14.517 --C age.mat \ --sim mc-full 1 2 lh.gender_age.glmdir/csd1 Do I add the --cache 4 neg \ --overwrite at the end? 5) When I run tksurfer to view the sig.mgh file and I set the threshold to 2, meaning vertices with p.01, I have just few vertices coloured in blue. Does this mean a low activation? If yes, what I have to do? Thank you very much! Antonella From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 17, 2011 11:53 AM Subject: Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: Dear Doug, Thank you very much for your valuable reply. I still have few questions on which I would like to ask your advise: QUESTION 1: While running the recall-all for all my subjects I also used the -qcache option. I am not sure how this data is further used for my GLM analysis. I will appreciate if you can confirm if in this case in order to do a thickness-age correlation group study I need to complete the following steps: STEP 1: Uncached Data: resamples each subjects data to fsaveragea (into a common space), and Concatenating all the subjects' into a single file by running mris_preproc --fsgd AGE_fsgd.fsgd \ --target fsaverage --hemi lh \ --meas thickness \ --out lh.AGE.thickness.00.mgh STEP 2: The independent variable is the thickness smoothed at various FWHM (full-width/half-max), usually 0, 5, 10, 10, 20, and 25mm so run: mris_preproc --fsgd AGE_fsgd.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.AGE.thickness.10.mgh STEP 3: If I run the next step (I know is optional) where I can use this data lh.AGE.thickness.10B.mgh? Is this a better data to be use for my further steps? You would use it in the same place that you would use lh.AGE.thickness.10.mgh. It is just a different way to compute it if you did not qcache. OPTIONAL: THIS WILL TAKE ABOUT 5 MINUTES mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.AGE.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.AGE.thickness.10B.mgh STEP 4: GLM Analysis (mri_glmfit) mri_glmfit \ --y lh.AGE.thickness.10.mgh \ --fsgd AGE_fsgd.fsgd dods\ --C lh-Avg-thickness-age-Cor.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.AGE.glmdir STEP 5: View the uncorrected significance map with tksurfer: tksurfer fsaverage lh inflated \ -annot aparc.annot -fthresh 2 \ -overlay lh.AGE.glmdir/lh-Avg-thickness-age-Cor/sig.mgh STEP 6: Viewing the medial surface, change the overlay threshold to something very, very low (say, .01), View -- Configure -- Overlay, set Min .01 STEP 7: CSD (Cluster Simulation Data)- Run the Simulation mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg \ --overwrite QUESTION 2: You mentioned that I should use the --cache option to mri_glmfit-sim. How I should do this? Do I need to change STEP 7? Yes, use mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --cache 4 neg \ --overwrite QUESTION 3: How I can check my data to make sure that I have actual activation above the voxel-wise threshold and how I can change my threshold? Based on what I need to change my threshold? Do I change my treshold until I find some activation? Run tksurfer to view the sig.mgh file. Set the threshold to the one you used in mri_glmfit-sim using the
Re: [Freesurfer] mri_glmfit-sim
Antonella Kis wrote: Hi Doug, Thanks again for your help. There are few more things not very clear for me and I will be very graetful if you can advise me: 1). Did you mean that if I did not qcache my data while I was doing pre-processing running the recon-all I should use then lh.AGE.thickness.10B.mgh? yes 2) Are then the mentioned steps the right one to be followed? yes 3) I saw on one tutorial about the mri_glm to perform estimations. What are this estimations? Do I need to run: Where did you see reference to mris_glm? This is an old program that we should not even distribute. # For the left hemisphere mris_glm --surfmeas thickness \ --hemi lh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100lh.mgz\ --var ./var_doss-thickness-100lh.mgz \ --y ./y_doss-thickness-100lh_000.mgz \ --nsmooth 100 # For the right hemisphere mris_glm --surfmeas thickness \ --hemi rh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100rh.mgz \ --var ./var_doss-thickness-100rh.mgz \ --y ./y_doss-thickness-100rh_000.mgz \ --nsmooth 100 4) If I have less than 80 subjects do I need to run the full MC simulation and I must supply the smoothest of my data as fwhm from the y.fsgd file? Also I would need to mention the threshold like in the following example? Yes. You are better off using mri_glmfit-sim rather than the command line below. mri_glmfit-sim will run that program giving it the appropriate fwhm. mri_glmfit --y lh.gender_age.thickness.10.mgh \ --glmdir lh.gender_age.glmdir \ --fsgd gender_age.txt doss \ --surf fsaverage lh \ --fwhm 14.517 --C age.mat \ --sim mc-full 1 2 lh.gender_age.glmdir/csd1 Do I add the --cache 4 neg \ --overwrite at the end? 5) When I run tksurfer to view the sig.mgh file and I set the threshold to 2, meaning vertices with p.01, I have just few vertices coloured in blue. Does this mean a low activation? If yes, what I have to do? Yes. You can try lowering it to 1.3 (p.05). If the effect is too subtle, you will need to add more subjects (assuming there is an effect at all). doug Thank you very much! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 17, 2011 11:53 AM *Subject:* Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: Dear Doug, Thank you very much for your valuable reply. I still have few questions on which I would like to ask your advise: QUESTION 1: While running the recall-all for all my subjects I also used the -qcache option. I am not sure how this data is further used for my GLM analysis. I will appreciate if you can confirm if in this case in order to do a thickness-age correlation group study I need to complete the following steps: STEP 1: Uncached Data: resamples each subjects data to fsaveragea (into a common space), and Concatenating all the subjects' into a single file by running mris_preproc --fsgd AGE_fsgd.fsgd \ --target fsaverage --hemi lh \ --meas thickness \ --out lh.AGE.thickness.00.mgh STEP 2: The independent variable is the thickness smoothed at various FWHM (full-width/half-max), usually 0, 5, 10, 10, 20, and 25mm so run: mris_preproc --fsgd AGE_fsgd.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.AGE.thickness.10.mgh STEP 3: If I run the next step (I know is optional) where I can use this data lh.AGE.thickness.10B.mgh? Is this a better data to be use for my further steps? You would use it in the same place that you would use lh.AGE.thickness.10.mgh. It is just a different way to compute it if you did not qcache. OPTIONAL: THIS WILL TAKE ABOUT 5 MINUTES mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.AGE.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.AGE.thickness.10B.mgh STEP 4: GLM Analysis (mri_glmfit) mri_glmfit \ --y lh.AGE.thickness.10.mgh \ --fsgd AGE_fsgd.fsgd dods\ --C lh-Avg-thickness-age-Cor.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.AGE.glmdir STEP 5: View the uncorrected significance map with tksurfer: tksurfer fsaverage lh inflated \ -annot aparc.annot -fthresh 2 \ -overlay lh.AGE.glmdir/lh-Avg-thickness-age-Cor/sig.mgh STEP 6: Viewing the medial surface, change the overlay threshold to something very, very low (say, .01), View -- Configure -- Overlay, set Min .01 STEP 7: CSD (Cluster Simulation Data)- Run the Simulation mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg \
Re: [Freesurfer] mri_glmfit-sim
Dear Doug, Thank you very much! I am ready to start doing my analysis but before I start you were mentioning that for the simulation 10,000 is a good number. You also suggested me to run: mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --cache 4 neg \ --overwrite but what is the number of the iteration if I run this part? Do I need to add this and do I need to mention the threshold in the above coding? THANKS! Antonella From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 17, 2011 1:10 PM Subject: Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: Hi Doug, Thanks again for your help. There are few more things not very clear for me and I will be very graetful if you can advise me: 1). Did you mean that if I did not qcache my data while I was doing pre-processing running the recon-all I should use then lh.AGE.thickness.10B.mgh? yes 2) Are then the mentioned steps the right one to be followed? yes 3) I saw on one tutorial about the mri_glm to perform estimations. What are this estimations? Do I need to run: Where did you see reference to mris_glm? This is an old program that we should not even distribute. # For the left hemisphere mris_glm --surfmeas thickness \ --hemi lh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100lh.mgz\ --var ./var_doss-thickness-100lh.mgz \ --y ./y_doss-thickness-100lh_000.mgz \ --nsmooth 100 # For the right hemisphere mris_glm --surfmeas thickness \ --hemi rh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100rh.mgz \ --var ./var_doss-thickness-100rh.mgz \ --y ./y_doss-thickness-100rh_000.mgz \ --nsmooth 100 4) If I have less than 80 subjects do I need to run the full MC simulation and I must supply the smoothest of my data as fwhm from the y.fsgd file? Also I would need to mention the threshold like in the following example? Yes. You are better off using mri_glmfit-sim rather than the command line below. mri_glmfit-sim will run that program giving it the appropriate fwhm. mri_glmfit --y lh.gender_age.thickness.10.mgh \ --glmdir lh.gender_age.glmdir \ --fsgd gender_age.txt doss \ --surf fsaverage lh \ --fwhm 14.517 --C age.mat \ --sim mc-full 1 2 lh.gender_age.glmdir/csd1 Do I add the --cache 4 neg \ --overwrite at the end? 5) When I run tksurfer to view the sig.mgh file and I set the threshold to 2, meaning vertices with p.01, I have just few vertices coloured in blue. Does this mean a low activation? If yes, what I have to do? Yes. You can try lowering it to 1.3 (p.05). If the effect is too subtle, you will need to add more subjects (assuming there is an effect at all). doug Thank you very much! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 17, 2011 11:53 AM *Subject:* Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: Dear Doug, Thank you very much for your valuable reply. I still have few questions on which I would like to ask your advise: QUESTION 1: While running the recall-all for all my subjects I also used the -qcache option. I am not sure how this data is further used for my GLM analysis. I will appreciate if you can confirm if in this case in order to do a thickness-age correlation group study I need to complete the following steps: STEP 1: Uncached Data: resamples each subjects data to fsaveragea (into a common space), and Concatenating all the subjects' into a single file by running mris_preproc --fsgd AGE_fsgd.fsgd \ --target fsaverage --hemi lh \ --meas thickness \ --out lh.AGE.thickness.00.mgh STEP 2: The independent variable is the thickness smoothed at various FWHM (full-width/half-max), usually 0, 5, 10, 10, 20, and 25mm so run: mris_preproc --fsgd AGE_fsgd.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.AGE.thickness.10.mgh STEP 3: If I run the next step (I know is optional) where I can use this data lh.AGE.thickness.10B.mgh? Is this a better data to be use for my further steps? You would use it in the same place that you would use lh.AGE.thickness.10.mgh. It is just a different way to compute it if you did not qcache. OPTIONAL: THIS WILL TAKE ABOUT 5 MINUTES mri_surf2surf --hemi lh \ --s fsaverage \ --sval lh.AGE.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.AGE.thickness.10B.mgh STEP 4: GLM Analysis (mri_glmfit)
Re: [Freesurfer] mri_glmfit-sim
for the cache, the simulation has already been done (using 10,000). This makes it much faster:). doug Antonella Kis wrote: Dear Doug, Thank you very much! I am ready to start doing my analysis but before I start you were mentioning that for the simulation 10,000 is a good number. You also suggested me to run: mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --cache 4 neg \ --overwrite but what is the number of the iteration if I run this part? Do I need to add this and do I need to mention the threshold in the above coding? THANKS! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 17, 2011 1:10 PM *Subject:* Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: Hi Doug, Thanks again for your help. There are few more things not very clear for me and I will be very graetful if you can advise me: 1). Did you mean that if I did not qcache my data while I was doing pre-processing running the recon-all I should use then lh.AGE.thickness.10B.mgh? yes 2) Are then the mentioned steps the right one to be followed? yes 3) I saw on one tutorial about the mri_glm to perform estimations. What are this estimations? Do I need to run: Where did you see reference to mris_glm? This is an old program that we should not even distribute. # For the left hemisphere mris_glm --surfmeas thickness \ --hemi lh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100lh.mgz\ --var ./var_doss-thickness-100lh.mgz \ --y ./y_doss-thickness-100lh_000.mgz \ --nsmooth 100 # For the right hemisphere mris_glm --surfmeas thickness \ --hemi rh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100rh.mgz \ --var ./var_doss-thickness-100rh.mgz \ --y ./y_doss-thickness-100rh_000.mgz \ --nsmooth 100 4) If I have less than 80 subjects do I need to run the full MC simulation and I must supply the smoothest of my data as fwhm from the y.fsgd file? Also I would need to mention the threshold like in the following example? Yes. You are better off using mri_glmfit-sim rather than the command line below. mri_glmfit-sim will run that program giving it the appropriate fwhm. mri_glmfit --y lh.gender_age.thickness.10.mgh \ --glmdir lh.gender_age.glmdir \ --fsgd gender_age.txt doss \ --surf fsaverage lh \ --fwhm 14.517 --C age.mat \ --sim mc-full 1 2 lh.gender_age.glmdir/csd1 Do I add the --cache 4 neg \ --overwrite at the end? 5) When I run tksurfer to view the sig.mgh file and I set the threshold to 2, meaning vertices with p.01, I have just few vertices coloured in blue. Does this mean a low activation? If yes, what I have to do? Yes. You can try lowering it to 1.3 (p.05). If the effect is too subtle, you will need to add more subjects (assuming there is an effect at all). doug Thank you very much! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 17, 2011 11:53 AM *Subject:* Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: Dear Doug, Thank you very much for your valuable reply. I still have few questions on which I would like to ask your advise: QUESTION 1: While running the recall-all for all my subjects I also used the -qcache option. I am not sure how this data is further used for my GLM analysis. I will appreciate if you can confirm if in this case in order to do a thickness-age correlation group study I need to complete the following steps: STEP 1: Uncached Data: resamples each subjects data to fsaveragea (into a common space), and Concatenating all the subjects' into a single file by running mris_preproc --fsgd AGE_fsgd.fsgd \ --target fsaverage --hemi lh \ --meas thickness \ --out lh.AGE.thickness.00.mgh STEP 2: The independent variable is the thickness smoothed at various FWHM (full-width/half-max), usually 0, 5, 10, 10, 20, and 25mm so run: mris_preproc --fsgd AGE_fsgd.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.AGE.thickness.10.mgh STEP 3: If I run the next step (I know is optional) where I can use this data lh.AGE.thickness.10B.mgh? Is
[Freesurfer] register data to the surface
Hi! I successfully run the preprocessing on some polarangle data (preproc-sess -sf seesid -surface self lhrh -fwhm 5). Now I would like to do the subtraction between some runs and then to visualize this subtraction on the surface (so without to analyze the data with Fourier analysis). Does anybody know how to do that? Thanks! Francesca ___ 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] register data to the surface
Hi Francesca, can you be more specific about what you want to do? If you just want to subtract the raw data between runs, you can use fscalc. doug francesca strappini wrote: Hi! I successfully run the preprocessing on some polarangle data (preproc-sess -sf seesid -surface self lhrh -fwhm 5). Now I would like to do the subtraction between some runs and then to visualize this subtraction on the surface (so without to analyze the data with Fourier analysis). Does anybody know how to do that? Thanks! Francesca ___ 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 ___ 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] How to run a benchmark on GPU with FreeSufer?
I want to verify what's the performance of different GPUs using FreeSurfer as Benchmark App. Thanks, Leo Souza -Original Message- From: R Edgar [mailto:freesurfer@gmail.com] Sent: Wednesday, August 17, 2011 6:20 AM To: Leo Souza; Freesurfer Mailing List Cc: Douglas N Greve Subject: Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer? On Tue, Aug 16, 2011 at 1:42 PM, Leo Souza lso...@nvidia.com wrote: Does anyone knows how do I run a benchmark test on GPU with FreeSurfer and CUDA? Beyond running a comparison between [x] and [x]_cuda? If you want numbers on individual routines, then the cudatest directory holds a lot of test cases which will run one routine and compare timings (these are used by the tests under test_tm). Could you explain what information you're looking for? Richard --- This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. --- ___ 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_glmfit-sim
Dear Doug, This is my last question for today and I will be very grateful if you can give me your advise one more time. When I run the: mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --cache 4 neg \ --overwrite the threshold is 4 (I am not sure why and if it has to be less for example 1.3 as you suggested) and I get only 3 clusters in my cache.the4. neg.sig.cluster.summary file. When I load the cluster annotation in tksurfer do I need to set the same threshold? tksurfer fsaverage lh inflated \ -annot lh.age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot \ -fthresh 2 -curv -gray I cannot see any colours/clusters on the inflated surface. If I change in the mri_glmfit-sim the threshold to 1.3 I am getting 5 clusters and still nothing when I load the cluster annotation in tksurfer. I am doing maybe something wrong or i just need more subjects? Thank you very much! Antonella From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 17, 2011 2:55 PM Subject: Re: [Freesurfer] mri_glmfit-sim for the cache, the simulation has already been done (using 10,000). This makes it much faster:). doug Antonella Kis wrote: Dear Doug, Thank you very much! I am ready to start doing my analysis but before I start you were mentioning that for the simulation 10,000 is a good number. You also suggested me to run: mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --cache 4 neg \ --overwrite but what is the number of the iteration if I run this part? Do I need to add this and do I need to mention the threshold in the above coding? THANKS! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 17, 2011 1:10 PM *Subject:* Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: Hi Doug, Thanks again for your help. There are few more things not very clear for me and I will be very graetful if you can advise me: 1). Did you mean that if I did not qcache my data while I was doing pre-processing running the recon-all I should use then lh.AGE.thickness.10B.mgh? yes 2) Are then the mentioned steps the right one to be followed? yes 3) I saw on one tutorial about the mri_glm to perform estimations. What are this estimations? Do I need to run: Where did you see reference to mris_glm? This is an old program that we should not even distribute. # For the left hemisphere mris_glm --surfmeas thickness \ --hemi lh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100lh.mgz\ --var ./var_doss-thickness-100lh.mgz \ --y ./y_doss-thickness-100lh_000.mgz \ --nsmooth 100 # For the right hemisphere mris_glm --surfmeas thickness \ --hemi rh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100rh.mgz \ --var ./var_doss-thickness-100rh.mgz \ --y ./y_doss-thickness-100rh_000.mgz \ --nsmooth 100 4) If I have less than 80 subjects do I need to run the full MC simulation and I must supply the smoothest of my data as fwhm from the y.fsgd file? Also I would need to mention the threshold like in the following example? Yes. You are better off using mri_glmfit-sim rather than the command line below. mri_glmfit-sim will run that program giving it the appropriate fwhm. mri_glmfit --y lh.gender_age.thickness.10.mgh \ --glmdir lh.gender_age.glmdir \ --fsgd gender_age.txt doss \ --surf fsaverage lh \ --fwhm 14.517 --C age.mat \ --sim mc-full 1 2 lh.gender_age.glmdir/csd1 Do I add the --cache 4 neg \ --overwrite at the end? 5) When I run tksurfer to view the sig.mgh file and I set the threshold to 2, meaning vertices with p.01, I have just few vertices coloured in blue. Does this mean a low activation? If yes, what I have to do? Yes. You can try lowering it to 1.3 (p.05). If the effect is too subtle, you will need to add more subjects (assuming there is an effect at all). doug Thank you very much! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 17, 2011 11:53 AM *Subject:* Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: Dear Doug, Thank
Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer?
On Wed, Aug 17, 2011 at 3:19 PM, Leo Souza lso...@nvidia.com wrote: I want to verify what's the performance of different GPUs using FreeSurfer as Benchmark App. In that case, the two best programs to run are mri_em_register[_cuda] for linear registration mri_ca_register[_cuda] for nonlinear registration You should know that Freesurfer quite likes the Nehalem memory hardware, whether in CPU or GPU mode. Also, mri_em_register_cuda has an additional pair of 'fast' options which cut the runtime even more (look at the top of the source file), but will sometimes give a different registration to the CPU version. Richard ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Error loading annot file
Hi Doug, Can be the reason that while getting 5 clusters and loading the annotation in tksurfer shows me nothing because I got the following error? Could not read annot file lh.age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot No such file or directory ERROR: could not load lh.age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot How can I fix this error? THANKS! Antonella From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 17, 2011 2:55 PM Subject: Re: [Freesurfer] mri_glmfit-sim for the cache, the simulation has already been done (using 10,000). This makes it much faster:). doug Antonella Kis wrote: Dear Doug, Thank you very much! I am ready to start doing my analysis but before I start you were mentioning that for the simulation 10,000 is a good number. You also suggested me to run: mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --cache 4 neg \ --overwrite but what is the number of the iteration if I run this part? Do I need to add this and do I need to mention the threshold in the above coding? THANKS! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 17, 2011 1:10 PM *Subject:* Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: Hi Doug, Thanks again for your help. There are few more things not very clear for me and I will be very graetful if you can advise me: 1). Did you mean that if I did not qcache my data while I was doing pre-processing running the recon-all I should use then lh.AGE.thickness.10B.mgh? yes 2) Are then the mentioned steps the right one to be followed? yes 3) I saw on one tutorial about the mri_glm to perform estimations. What are this estimations? Do I need to run: Where did you see reference to mris_glm? This is an old program that we should not even distribute. # For the left hemisphere mris_glm --surfmeas thickness \ --hemi lh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100lh.mgz\ --var ./var_doss-thickness-100lh.mgz \ --y ./y_doss-thickness-100lh_000.mgz \ --nsmooth 100 # For the right hemisphere mris_glm --surfmeas thickness \ --hemi rh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100rh.mgz \ --var ./var_doss-thickness-100rh.mgz \ --y ./y_doss-thickness-100rh_000.mgz \ --nsmooth 100 4) If I have less than 80 subjects do I need to run the full MC simulation and I must supply the smoothest of my data as fwhm from the y.fsgd file? Also I would need to mention the threshold like in the following example? Yes. You are better off using mri_glmfit-sim rather than the command line below. mri_glmfit-sim will run that program giving it the appropriate fwhm. mri_glmfit --y lh.gender_age.thickness.10.mgh \ --glmdir lh.gender_age.glmdir \ --fsgd gender_age.txt doss \ --surf fsaverage lh \ --fwhm 14.517 --C age.mat \ --sim mc-full 1 2 lh.gender_age.glmdir/csd1 Do I add the --cache 4 neg \ --overwrite at the end? 5) When I run tksurfer to view the sig.mgh file and I set the threshold to 2, meaning vertices with p.01, I have just few vertices coloured in blue. Does this mean a low activation? If yes, what I have to do? Yes. You can try lowering it to 1.3 (p.05). If the effect is too subtle, you will need to add more subjects (assuming there is an effect at all). doug Thank you very much! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 17, 2011 11:53 AM *Subject:* Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: Dear Doug, Thank you very much for your valuable reply. I still have few questions on which I would like to ask your advise: QUESTION 1: While running the recall-all for all my subjects I also used the -qcache option. I am not sure how this data is further used for my GLM analysis. I will appreciate if you can confirm if in this case in order to do a thickness-age correlation group study I need to complete the following steps: STEP 1: Uncached Data: resamples each
Re: [Freesurfer] mri_glmfit-sim
Antonella Kis wrote: Dear Doug, This is my last question for today and I will be very grateful if you can give me your advise one more time. When I run the: mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --cache 4 neg \ --overwrite the threshold is 4 (I am not sure why and if it has to be less for example 1.3 as you suggested) and I get only 3 clusters in my cache.the4. neg.sig.cluster.summary file. This threshold is somewhat arbitrary (a criticism of this method). The answer to which threshold is right is partially a question of power (meaning that you can't answer it for a given data set). It also needs to be above some minimum to make the stats work out better (I would not go lower than 1.3). When I load the cluster annotation in tksurfer do I need to set the same threshold? tksurfer fsaverage lh inflated \ -annot lh.age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot \ -fthresh 2 -curv -gray I cannot see any colours/clusters on the inflated surface. If I change in the mri_glmfit-sim the threshold to 1.3 I am getting 5 clusters and still nothing when I load the cluster annotation in tksurfer. I am doing maybe something wrong or i just need more subjects? That tksurfer command loads them as an annotation, not as a statistical overlay, so the threshold will have no effect. If you want an overlay, try looking at the ...sig.cluster.mgh file (this will be redundant with the annot). doug Thank you very much! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 17, 2011 2:55 PM *Subject:* Re: [Freesurfer] mri_glmfit-sim for the cache, the simulation has already been done (using 10,000). This makes it much faster:). doug Antonella Kis wrote: Dear Doug, Thank you very much! I am ready to start doing my analysis but before I start you were mentioning that for the simulation 10,000 is a good number. You also suggested me to run: mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --cache 4 neg \ --overwrite but what is the number of the iteration if I run this part? Do I need to add this and do I need to mention the threshold in the above coding? THANKS! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 17, 2011 1:10 PM *Subject:* Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: Hi Doug, Thanks again for your help. There are few more things not very clear for me and I will be very graetful if you can advise me: 1). Did you mean that if I did not qcache my data while I was doing pre-processing running the recon-all I should use then lh.AGE.thickness.10B.mgh? yes 2) Are then the mentioned steps the right one to be followed? yes 3) I saw on one tutorial about the mri_glm to perform estimations. What are this estimations? Do I need to run: Where did you see reference to mris_glm? This is an old program that we should not even distribute. # For the left hemisphere mris_glm --surfmeas thickness \ --hemi lh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100lh.mgz\ --var ./var_doss-thickness-100lh.mgz \ --y ./y_doss-thickness-100lh_000.mgz \ --nsmooth 100 # For the right hemisphere mris_glm --surfmeas thickness \ --hemi rh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100rh.mgz \ --var ./var_doss-thickness-100rh.mgz \ --y ./y_doss-thickness-100rh_000.mgz \ --nsmooth 100 4) If I have less than 80 subjects do I need to run the full MC simulation and I must supply the smoothest of my data as fwhm from the y.fsgd file? Also I would need to mention the threshold like in the following example? Yes. You are better off using mri_glmfit-sim rather than the command line below. mri_glmfit-sim will run that program giving it the appropriate fwhm. mri_glmfit --y lh.gender_age.thickness.10.mgh \ --glmdir lh.gender_age.glmdir \ --fsgd gender_age.txt doss \ --surf fsaverage lh \ --fwhm 14.517 --C age.mat \ --sim mc-full 1 2 lh.gender_age.glmdir/csd1 Do I add the --cache 4 neg \ --overwrite at the end? 5) When I run tksurfer to view the sig.mgh file and I set the
Re: [Freesurfer] Error loading annot file
Use ./lh.age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot (note the leading ./) Antonella Kis wrote: Hi Doug, Can be the reason that while getting 5 clusters and loading the annotation in tksurfer shows me nothing because I got the following error? Could not read annot file lh.age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot No such file or directory ERROR: could not load lh.age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot How can I fix this error? THANKS! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 17, 2011 2:55 PM *Subject:* Re: [Freesurfer] mri_glmfit-sim for the cache, the simulation has already been done (using 10,000). This makes it much faster:). doug Antonella Kis wrote: Dear Doug, Thank you very much! I am ready to start doing my analysis but before I start you were mentioning that for the simulation 10,000 is a good number. You also suggested me to run: mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --cache 4 neg \ --overwrite but what is the number of the iteration if I run this part? Do I need to add this and do I need to mention the threshold in the above coding? THANKS! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 17, 2011 1:10 PM *Subject:* Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: Hi Doug, Thanks again for your help. There are few more things not very clear for me and I will be very graetful if you can advise me: 1). Did you mean that if I did not qcache my data while I was doing pre-processing running the recon-all I should use then lh.AGE.thickness.10B.mgh? yes 2) Are then the mentioned steps the right one to be followed? yes 3) I saw on one tutorial about the mri_glm to perform estimations. What are this estimations? Do I need to run: Where did you see reference to mris_glm? This is an old program that we should not even distribute. # For the left hemisphere mris_glm --surfmeas thickness \ --hemi lh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100lh.mgz\ --var ./var_doss-thickness-100lh.mgz \ --y ./y_doss-thickness-100lh_000.mgz \ --nsmooth 100 # For the right hemisphere mris_glm --surfmeas thickness \ --hemi rh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100rh.mgz \ --var ./var_doss-thickness-100rh.mgz \ --y ./y_doss-thickness-100rh_000.mgz \ --nsmooth 100 4) If I have less than 80 subjects do I need to run the full MC simulation and I must supply the smoothest of my data as fwhm from the y.fsgd file? Also I would need to mention the threshold like in the following example? Yes. You are better off using mri_glmfit-sim rather than the command line below. mri_glmfit-sim will run that program giving it the appropriate fwhm. mri_glmfit --y lh.gender_age.thickness.10.mgh \ --glmdir lh.gender_age.glmdir \ --fsgd gender_age.txt doss \ --surf fsaverage lh \ --fwhm 14.517 --C age.mat \ --sim mc-full 1 2 lh.gender_age.glmdir/csd1 Do I add the --cache 4 neg \ --overwrite at the end? 5) When I run tksurfer to view the sig.mgh file and I set the threshold to 2, meaning vertices with p.01, I have just few vertices coloured in blue. Does this mean a low activation? If yes, what I have to do? Yes. You can try lowering it to 1.3 (p.05). If the effect is too subtle, you will need to add more subjects (assuming there is an effect at all). doug Thank you very much! Antonella *From:* 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 *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
[Freesurfer] outline of a label as an overlay
Hello All, Is there a way to save the outline of a label as an overlay (say .mgh file) ? Please let me know. Thanks Ri ___ 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] register data to the surface
Sorry, I try to be more specific. I would like to be able to take the volume-to-surface transformation calculated on one set of functional data, and apply that transformation to another set of functional data (the subtraction) of the same subject. This will allow me to display arbitrary functional values on a surface. Thanks! Francesca ___ 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] register data to the surface
You can use bbregister to compute the transformation for each run based on the middle time point of that run (and assuming you've motion corrected the run), then use mri_vol2surf to resample any data set aligned with the middle time point to the subject's surface or the fsaverage surface. You can do that for each run separately, then use fscalc to compute the difference. doug francesca strappini wrote: Sorry, I try to be more specific. I would like to be able to take the volume-to-surface transformation calculated on one set of functional data, and apply that transformation to another set of functional data (the subtraction) of the same subject. This will allow me to display arbitrary functional values on a surface. Thanks! Francesca -- 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 ___ 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] tksurfer retinotopy analysis vs auto parcellation of V1/V2
You might need to smooth even more. Michelle Umali wrote: Dear Bruce Doug, Thanks I'll do the label comparison. I am attaching a fieldsign pic to show the irregularity of the blue/red bands. Can you suggest a method of determining V1/2/3 based on the odd pattern? Thank you very much. Michelle they have to overlap unless the classification was 100% accurate with no variability. You can just pick the label with the highest probability at each vertex Quoting Douglas N Greve gr...@nmr.mgh.harvard.edu: can you send a pic? Michelle Umali wrote: Hi Doug, So I did the additional smoothing and the map looks better.. It's still hard to interpret though. I was expecting alternating red and blue bands to signify V1/V2/V3 boundaries, but it's very irregular with red curves running every which way into blue splotches. Do you have any suggestions how to interpret this? So then I just looked at the automatic parcellation of V1 and V2, which seems very different from the actual fieldsign results.. The boundaries overlap quite a bit, which seems odd. How should I treat the overlap? Thanks for your help. Michelle Alsouoting Douglas N Greve gr...@nmr.mgh.harvard.edu: Michelle Umali wrote: Hi Doug, I've already smoothed by 5 during preproc-sess, so does this mean I should do additional smoothing during fieldsign-sess step? Try the additional one now to see if it fixes the map. Also, is this the correct command to use the sphere and not the patch: fieldsign-sess -a rtopy.self.lh -fwhm 5 -sphere -s sj09 yes doug Thanks. Michelle Quoting Douglas N Greve gr...@nmr.mgh.harvard.edu: Try smoothing (eg, -fwhm 5) when running fieldsign-sess. You can also try using the sphere instead of the occip patch. doug Michelle Umali wrote: Hi Doug, Thanks again for your advice, the heat maps look much better. However, they still do not visualize the continuous range of angles or eccentricities but rather divide it into two intervals such as red vs. blue. Is there any way to adjust the color range to make it more appropriate for this kind of data? The heat map for the field sign data still looks speckled. I attached an image showing the heat maps for polar angle, eccentricity, and field sign, with the corresponding overlay settings. I used 5mm smoothing. Thank you very much, Michelle Quoting Douglas N Greve gr...@nmr.mgh.harvard.edu: The activation looks pretty reasonable. As you point out, the angles are a mess. How did you set the color scale for the angles? You should leave it as a heat scale (if you're using tksurfer-sess). How much did you smooth? doug Michelle Umali wrote: Hi Doug, Attached is a pic of the significance and angle maps for polar and eccen. What do you think? Thanks. Michelle Quoting Douglas N Greve gr...@nmr.mgh.harvard.edu: what does the activation look like? Does it look right? Can you send a pic? doug Michelle Umali wrote: Hi Doug, The z-values are consistently near or greater than 4. It just seems that the visualization of the angles is somehow incorrect... Is there be anything else that I need to check? Thanks. Michelle ___ 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 The information in this e-mail is intended only for the personto whom it is addressed. If you believe this e-mail was sent to you in errorand the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html - End forwarded message - ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] pial surface documentation
Where may I find the documentation explaining the content and format of the pial and gray-white surface files? Thanks, -Jeff ___ 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] voxel assignment error in V1
This is the polar angle map? What does it look like inflated? Do you acquire data with the wedge going in both directions? Even if you do, there can be some delay errors that creep in. doug Ritobrato Datta wrote: Hello All, We have processed retinotopy data and piped the phase maps into freesurfer stream. As can be seen on the attached reconstructed image, there are patches of cortex (some reds) within the calcarine sulcus that are wrongly assigned to the upper bank. Any ideas on how to correct for these mis-identified patches in FreeSurfer ? I have already checked using tkregister the registration of the functional data to the freesurfer anatomy and that looks fine. Please let me know Thanks Ri ___ 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 ___ 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] outline of a label as an overlay
not that I know of. You can convert it to an annotation (mris_label2annot) and then view the annot in outline mode. Ritobrato Datta wrote: Hello All, Is there a way to save the outline of a label as an overlay (say .mgh file) ? Please let me know. Thanks Ri ___ 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 ___ 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] How to run a benchmark on GPU with FreeSufer?
Can you provide quick instructions on how to run those tests? I am new to FreeSurfer. Thanks, Leo Souza -Original Message- From: R Edgar [mailto:freesurfer@gmail.com] Sent: Wednesday, August 17, 2011 12:36 PM To: Leo Souza Cc: Freesurfer Mailing List; Douglas N Greve Subject: Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer? On Wed, Aug 17, 2011 at 3:19 PM, Leo Souza lso...@nvidia.com wrote: I want to verify what's the performance of different GPUs using FreeSurfer as Benchmark App. In that case, the two best programs to run are mri_em_register[_cuda] for linear registration mri_ca_register[_cuda] for nonlinear registration You should know that Freesurfer quite likes the Nehalem memory hardware, whether in CPU or GPU mode. Also, mri_em_register_cuda has an additional pair of 'fast' options which cut the runtime even more (look at the top of the source file), but will sometimes give a different registration to the CPU version. Richard --- This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. --- ___ 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] FMRI Asymmetry Analyses
Hello-
Trying this post again. I would like to directly compare
asymmetries in FMRI activation in surface space based on the Greve et al
poster presented at HBM this year. We would like to register each subject’s
T1 data to the contralateral hemisphere of fsaverage and made templates of
the contra (?h.con.sphere.reg ) and ipsilateral (?h.sphere.reg )
registrations. Is the following correct for the cross hemisphere
registration? Thanks
mris_register -reverse -curv surf/rh.sphere
{$FREESURFER_HOME}/average/lh.average.curvature.filled.buckner40.tif
surf/rh.CON.sphere.reg
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Re: [Freesurfer] FMRI Asymmetry Analyses
I don't have any docs set up and ready to use, but here are some
instructions that should get you started.
doug
---
Download these files
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gz
# Copy surfreg and xhemireg into $FREESURFER_HOME/bin
# Untar fsaverage_sym.tar.gz into your $SUBJECTS_DIR
cd $SUBJECTS_DIR
tar xvfz fsaverage_sym.tar.gz
-
To apply an existing atlas (eg, fsaverage_sym) to an anatomical analysis
# Reg to atlas (1-2 hours per subject)
# Creates $subject/xhemi
# Creates lh.fsaverage_sym.sphere.reg in $subject and $subject/xhemi
foreach subject (subjectlist)
surfreg --s $subject --t fsaverage_sym --lh
surfreg --s $subject --t fsaverage_sym --lh --xhemi
end
# Create a stack of subjects
mris_preproc --target fsaverage_sym --hemi lh
--xhemi --paired-diff \
--srcsurfreg fsaverage_sym.sphere.reg \
--meas thickness \
--out lh.lh-rh.thickness.sm00.mgh \
--s subj1 --s subj2 ...
# Smooth
mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm 5\
--i lh.lh-rh.thickness.sm00.mgh --o lh.lh-rh.thickness.sm05.mgh
# Test
mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir
glm.lh.lh-rh.thickness.sm05 \
--osgm --surf fsaverage_sym lh
# View
tksurfer fsaverage_sym lh inflated -aparc -overlay
glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh
# Correct for MC (need new version of mri_glmfit-sim)
mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 \
--cwpvalthresh .5 --cache 2 abs \
--subject-override fsaverage
-
# To apply an existing atlas to an arbitray volume data set:
bbregister --s subject --reg register.dat ...
mri_vol2surf --reg register.dat --mov data.nii.gz --hemi lh --o data.lh.nii
mri_vol2surf --reg register.dat --mov data.nii.gz --hemi rh --o data.rh.nii
# Map lh data to fsaverage_sym
mri_surf2surf --srcsubject subject --srcsurfreg fsaverage_sym.sphere.reg \
--trgsubject fsaverage_sym --trgsurfreg sphere.reg --hemi lh --sval
data.lh.nii \
--tval data.lh.fsaverage_sym.nii
# Map rh data to fsaverage_sym. Note: (1) subject is subject/xhemi
# and (2) The hemi (--hemi lh) is still lh not rh.
mri_surf2surf --srcsubject subject/xhemi --srcsurfreg
fsaverage_sym.sphere.reg \
--trgsubject fsaverage_sym --trgsurfreg sphere.reg --hemi lh --sval
data.rh.nii \
--tval data.rh.fsaverage_sym.nii
data.lh.fsaverage_sym.nii and data.rh.fsaverage_sym.nii are now in
voxel-for-voxel registration.
Andy Mayer wrote:
Hello-
Trying this post again. I would like to directly compare
asymmetries in FMRI activation in surface space based on the Greve et
al poster presented at HBM this year. We would like to register each
subject’s T1 data to the contralateral hemisphere of fsaverage and
made templates of the contra (?h.con.sphere.reg ) and ipsilateral
(?h.sphere.reg ) registrations. Is the following correct for the cross
hemisphere registration? Thanks
mris_register -reverse -curv surf/rh.sphere
{$FREESURFER_HOME}/average/lh.average.curvature.filled.buckner40.tif
surf/rh.CON.sphere.reg
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--
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
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Re: [Freesurfer] register data to the surface
Thanks a lot! I tried the registration with bbregister but unfortunately when I checked the result the functional volume was very distant from the target. Could I tried something else to improve the registration? I typed: bbregister --s subject --mov name_file.nii --reg register.dat --init-fsl --bold Thanks again! Francesca ___ 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] register data to the surface
It was probably the initialization that failed. To test this, run fslregister (very similar command line to bbregister). If that does not look good, then it is an init problem. If these were acquired in the same session, then you can try using --init-header. If you have spm installed, you can try --init-spm. The spm solution requires that SPM be set up properly for this program, which is not always so easy. It also requires matlab. doug francesca strappini wrote: Thanks a lot! I tried the registration with bbregister but unfortunately when I checked the result the functional volume was very distant from the target. Could I tried something else to improve the registration? I typed: bbregister --s subject --mov name_file.nii --reg register.dat --init-fsl --bold Thanks again! Francesca -- 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 ___ 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] pial surface documentation
Hi Jeff,
Not sure where you can find a verbose documentation, but you can figure
out by looking at the file read_surf.m in the ${FREESURFER_HOME}/matlab
directory. It's straightforward.
All the best,
Anderson
On 08/17/2011 04:32 PM, Jeff Eriksen wrote:
Where may I find the documentation explaining the content and format
of the pial and gray-white surface files? Thanks,
-Jeff
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[Freesurfer] tracula executables for snow leopard now online
Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into memory issues with the leopard version, you can download this, copy the new files into your $FREESURFER_HOME/bin, and try rerunning the part of the analysis that had errored out. Let us know if there are any problems, a.y ___ 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] pial surface documentation
self-documenting code :)
On Wed, 17 Aug 2011, Anderson Winkler wrote:
Hi Jeff,
Not sure where you can find a verbose documentation, but you can figure out
by looking at the file read_surf.m in the ${FREESURFER_HOME}/matlab
directory. It's straightforward.
All the best,
Anderson
On 08/17/2011 04:32 PM, Jeff Eriksen wrote:
Where may I find the documentation explaining the content and
format of the pial and gray-white surface files? Thanks,
-Jeff
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[Freesurfer] Problems Installing Freesurfer on an EC2 AMI
Hello, I'm trying to install FreeSurfer (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz) on an Ubuntu-10.04 x86_64 AMI hosted on Amazon's EC2, but after following the installation instructions I am unable to complete the Testing your Freesurfer Installation section. I am not trying to use any of the visualization tools, just recon-all -s bert -autorecon1 and the mri_tools, like mri_convert. I get the following error when I run recon-all -s bert -autorecon1 (recon-all.log attached) ... Found 3 runs /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz has frames ... I saw a previous post with the multi-frame error ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18444.html) and tried running mri_info to include in this email, but mri_info does not execute. Actually none of the mri_* tools are working and do not provide usage information when executed without any parameters. Any idea what I what I did wrong, or could this have to do with running freesurfer on EC2? Thanks for your help! Nolan recon-all.log Description: Binary data ___ 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] Problems Installing Freesurfer on an EC2 AMI
i havent seen this problem. i think others have run freesurfer on the amazon cloud before. the only thing i can think of, when you mention that the mri_* tools will not run (and in the recon-all.log, only the scripts printed their version info) is that the mri_* executables are all run through the UPX tool prior to distribution. this reduces their size, but maybe its having some weird effect on your system. if you have upx installed (Ultimate Packer for eXecutables), then you can run: upx -d mri_info to decompress mri_info (or mri_convert) then you might get some output when you run these commands. if so, then you would need to run upx -d on all the mri_* and mris_* executables. n. On Wed, 2011-08-17 at 20:50 -0700, Nolan Nichols wrote: Hello, I'm trying to install FreeSurfer (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz) on an Ubuntu-10.04 x86_64 AMI hosted on Amazon's EC2, but after following the installation instructions I am unable to complete the Testing your Freesurfer Installation section. I am not trying to use any of the visualization tools, just recon-all -s bert -autorecon1 and the mri_tools, like mri_convert. I get the following error when I run recon-all -s bert -autorecon1 (recon-all.log attached) ... Found 3 runs /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz has frames ... I saw a previous post with the multi-frame error (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18444.html) and tried running mri_info to include in this email, but mri_info does not execute. Actually none of the mri_* tools are working and do not provide usage information when executed without any parameters. Any idea what I what I did wrong, or could this have to do with running freesurfer on EC2? Thanks for your help! Nolan ___ 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.
