Re: [Freesurfer] visualize subcortical areas in tksurfer?
Hi Daniel I wouldn't advise this - you will miss most of the activation unless it happens to be right next to where the surface runs adjacent to the structure of interest. For subcortical structures you are better off showing the results in slices. cheers Bruce On Mon, 23 Feb 2015, Yang, Daniel wrote: Hi Bruce, Thanks for the reply. My main question is how to best visualize subcortical activation in a figure. Sometimes we do see some subcortical activation (like the attached, which is a random search) (if the attachment does not work, please see the examplehere: http://www.frontiersin.org/files/Articles/18483/fnhum-06-00021-HTML/ image_m/fnhum-06-00021-g003.jpg). Is it okay to visualize such subcortical activation via tksurfer? If not, could you please recommend a method to visualize subcortical activation? Sincerely, Daniel On 2/20/15, 9:06 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: HI Daniel no, that won't work. Vol2surf samples a volume to an existig surface and none of the subcortical structures will be anywere near the cortical surface. You would need to run mri_tessellate on each subcortical label that you want to generate a surface for, but I'm still not sure what you are trying to do. cheers Bruce On Fri, 20 Feb 2015, Yang, Daniel wrote: Hi Bruce, Thanks! and yes, I used mri_vol2surf to convert subcortical region as a volume file to surface (mgh file) and then visualize it with tksurfer. According to what you said, this is still valid, right? Best, Daniel On 2/19/15, 5:59 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Daniel no, tksurfer visualizes surfaces exclusively, and the subcortical structures are volumetric by and large. You could tesselate their surface and view it in tksurfer, or just use tkmediit or freeview. cheers Bruce On Thu, 19 Feb 2015, Yang, Daniel wrote: Dear FreeSurfer experts, I find that tksurfer allows me to visualize subcortical areas such as hippocampus. The visualization looks valid to me. Can tksurfer be used in this way? Thanks!! Daniel ___ 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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl iancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxz UZGOKpGXPDgqUHYm=GwXYm_UFsMTK666w58RNVUgITnGz6y7wSvA4OWe3VDIs=X6YOsg4F5k hF6_1eRhIIXjcpNfRIveb8xbtz9jVs7Rke= . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli ancelined=AwIBAgc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxzUZ GOKpGXPDgqUHYm=cue78znVQSK09ZAzgx1bpMEP_Q1FH_tPiP6u951nI6Is=FTUF8bxfkijut U0D90a6nXk4E6QXECVzI7RktBWSD04e= . 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] Using -qcache command multiple times
Hello, I had a question about using the -qcache command for smoothing. Previously, the -qcache command was used on several subjects in my dataset, and since then, these subjects have undergone some manual edits (control points, edits to wm.mgz, etc.). Currently, I’d like to run the -qcache command on the entire group of subjects – do I need to delete any files created by the previous uses of -qcache first, or is it ok just to go ahead and run the command for all subjects? Thank you, Anne Park ___ 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] Older version (5.0) on newer OSes
Hello everyone, I have a quick question about the feasibility of running FreeSurfer v5.0 on either RedHat/Centos 6.x or a newer Debian install. We want to run some new subjects but compare them to subjects run 5 yrs ago with FreeSurfer 5.0. Running all of the old subjects again in v5.3 is infeasible. I pulled down the Centos 5 binaries (just to try) but they segfault when running recon-all. I'd dedicate a machine to an older OS for compatibility, but we were hoping to use our NiPype pipeline, which works just fine with v 5.3 and is installed on the newer OSes. So - does anyone know if it's possible? TIA for any help. Cheers, Bill Ulrich ___ 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] treatment effect compare to controls
Hi, yes, the first is to stack all the data into a single file (on your study average, usually that is fsaverage). The second steps smoothes the data. You can use different smoothing levels, depending on your data. Usually 10 or 15 is a good number. The data will automatically be taken from the sub1t1.long.tempsub1 etc directories (this is signaled by the --qdec-long flag. The qdec table needs to be in the longitudinal format, that means the first column is the subject id (sub1-t1) the second column the base name (tempsub1) column headers are fsid fsid-base …. usually the third column is time from baseline (in years), but can be any time variable that you want to use in the LME. There is an example of the longitudinal qdec table here: http://freesurfer.net/fswiki/LongitudinalTwoStageModel I'll probably add that to the lme page so it is easier to find. Best, Martin On Feb 23, 2015, at 4:54 AM, amirhossein manzouri a.h.manzo...@gmail.com wrote: Hi and thanks Martin for your help, I am trying to do mixed effect analysis, should I use the registered to template data for this ( sub1-t1.long.tempsub1 and sub1-t2.long.tempsub1) and how should the aded.table.dat look like? Do I need to run : mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex --noreshape - Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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] confirm 5db71d8d19a634948b059d302f95d798f665a638
Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I get this error message: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd For the mkanalysis-sess i used fwhm = 5. When i do the same for mni305 and use: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166 It works well without an error. Thanks,Eiran On Monday, February 23, 2015 10:37 AM, freesurfer-requ...@nmr.mgh.harvard.edu freesurfer-requ...@nmr.mgh.harvard.edu wrote: Mailing list subscription confirmation notice for mailing list Freesurfer We have received a request from 79.177.55.71 for subscription of your email address, eiranha...@yahoo.com, to the freesurfer@nmr.mgh.harvard.edu mailing list. To confirm that you want to be added to this mailing list, simply reply to this message, keeping the Subject: header intact. Or visit this web page: https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/5db71d8d19a634948b059d302f95d798f665a638 Or include the following line -- and only the following line -- in a message to freesurfer-requ...@nmr.mgh.harvard.edu: confirm 5db71d8d19a634948b059d302f95d798f665a638 Note that simply sending a `reply' to this message should work from most mail readers, since that usually leaves the Subject: line in the right form (additional Re: text in the Subject: is okay). If you do not wish to be subscribed to this list, please simply disregard this message. If you think you are being maliciously subscribed to the list, or have any other questions, send them to freesurfer-ow...@nmr.mgh.harvard.edu. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_glmfit-sim Error
Hello Freesurfers, I use freesurfer v5.3.0 When I do group analysis correction for multiple comparisons for lh as follows: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz --surface fsaverage lh mri_glmfit-sim --glmdir group.glm --cache 3 pos --cwpvalthresh .0166 I get this error message: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm00/pos/th30/mc-z.csd For the mkanalysis-sess i used fwhm = 5. When i do the same for mni305 and use: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --glmdir group.glm --nii.gz mri_glmfit-sim --glmdir group.glm --grf 3 pos --cwpvalthresh .0166 It works well without an error. Thanks,Eiran___ 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] treatment effect compare to controls
Hi and thanks Martin for your help, I am trying to do mixed effect analysis, should I use the registered to template data for this ( sub1-t1.long.tempsub1 and sub1-t2.long.tempsub1) and how should the aded.table.dat look like? Do I need to run : mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex --noreshape ___ 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] RAM Replace
I would very much hope that replacing the RAM wouldn't change anything Bruce On Mon, 23 Feb 2015, Pedro Rosa - Gmail wrote: Dear all, I would like to know whether a RAM memory replacement in a Mac computer would change FreeSurfer 5.3 processing. I have a sample that was almost completely processed, but there are a few subjects whose acquisition are yet to be done. I would like know whether I could process such images after the RAM replacement without biasing the study. The change would be from a Markvision without ECC (error-correction code) to a Kingston with ECC. Thanks in advance, Pedro Rosa. ___ 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] RAM Replace
Thanks, Bruce. I am asking this because I believe that changing the processor or the operational system could change the processing. If I got it correctly, it is expected that it is not the same for the RAM. Am I correct? Thanks again, Pedro. On Feb 23, 2015, at 21:50, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I would very much hope that replacing the RAM wouldn't change anything Bruce On Mon, 23 Feb 2015, Pedro Rosa - Gmail wrote: Dear all, I would like to know whether a RAM memory replacement in a Mac computer would change FreeSurfer 5.3 processing. I have a sample that was almost completely processed, but there are a few subjects whose acquisition are yet to be done. I would like know whether I could process such images after the RAM replacement without biasing the study. The change would be from a Markvision without ECC (error-correction code) to a Kingston with ECC. Thanks in advance, Pedro Rosa. ___ 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
Re: [Freesurfer] RAM Replace
yes, it would be pretty strange if swapping out ram changed the results On Mon, 23 Feb 2015, Pedro Rosa wrote: Thanks, Bruce. I am asking this because I believe that changing the processor or the operational system could change the processing. If I got it correctly, it is expected that it is not the same for the RAM. Am I correct? Thanks again, Pedro. On Feb 23, 2015, at 21:50, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I would very much hope that replacing the RAM wouldn't change anything Bruce On Mon, 23 Feb 2015, Pedro Rosa - Gmail wrote: Dear all, I would like to know whether a RAM memory replacement in a Mac computer would change FreeSurfer 5.3 processing. I have a sample that was almost completely processed, but there are a few subjects whose acquisition are yet to be done. I would like know whether I could process such images after the RAM replacement without biasing the study. The change would be from a Markvision without ECC (error-correction code) to a Kingston with ECC. Thanks in advance, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] RAM Replace
Dear all, I would like to know whether a RAM memory replacement in a Mac computer would change FreeSurfer 5.3 processing. I have a sample that was almost completely processed, but there are a few subjects whose acquisition are yet to be done. I would like know whether I could process such images after the RAM replacement without biasing the study. The change would be from a Markvision without ECC (error-correction code) to a Kingston with ECC. Thanks in advance, Pedro Rosa. ___ 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.
