Re: [Freesurfer] FW: Surface Generation Problem Pertaining to FreeSurfer
You can generate a surface from the hippocampus by first running recon-all on an anatomical image, then using mri_mc to tessellate the left and right hippocampi. cheers Bruce On Tue, 22 Feb 2011, Saad Shakeel wrote: From: saad.ak...@hotmail.com To: fsregis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: Surface Generation Problem Pertaining to FreeSurfer Date: Tue, 22 Feb 2011 11:43:36 +0500 Hello, We are graduate students from Giki university, Pakistan. We are doing our Final Year Project on shape Analysis Techniques.Our Project steps area. Segmentation b. Surface Generation c. Spherical Harmonics for shape Analysis. We need your help pertaining to Surface Generation module. I have certain problems:1. How to create : surface generation of hippo-campus ( Exists In Sub-cortical region of Human Brain)2. Can I use mri_vol2surf tool in FreeSurfer for this purpose. If so, then what are the advantages and dis-advantages Thankyou for your time. Kindly send me the supporter's email address if you don't deal with this kind of situation. ___ 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] overlay sig.mgh onto T1 vol
Try loading it with the surfaces (add -surfs to your tkmedit cmd). It may be on the surface at that location. doug Fernanda Palhano wrote: Hi Doug, Thanks for the command, it worked well. But, I still have a problem. The overlay seems to be misplaced. I'm sending a .png with an example where cortical thickness appears in corpus callosum. To transform sig.mgh to vol I use: mri_surf2vol --surfval qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh --identity fsaverage --template fsaverage/mri/T1.mgz --hemi lh --o teste_sig.mgz Did I do something wrong? Any suggestions? Thanks again, On Mon, Feb 21, 2011 at 6:01 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: use tkmedit fsaverage orig.mgz -overlay teste_sig.mgz doug On 2/21/11 3:46 PM, Fernanda Palhano wrote: Hi Bruce, Thank you for the prompt reply. I tried using mri_surf2vol : mri_surf2vol --surfval qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh --identity fsaverage --template fsaverage/mri/T1.mgz --hemi lh --o teste_sig.mgz gdiagno = -1 Using identity matrix for registration Qa2v: SurfXYZ to VolCRS: -- -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; -- subjects dir /Applications/freesurfer/subjects/dados_Riba/ surface value path qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh hemi lh mksurfmask 0 projfrac 0 outvol path teste_sig.mgz template path fsaverage/mri/T1.mgz --- Anat2Vol Registration (TkReg) 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; - height = 256 width = 256 depth = 256 xsize = 1.00 ysize = 1.00 zsize = 1.00 cdc = -1.00 0.00 0.00 rdc = 0.00 0.00 -1.00 sdc = 0.00 1.00 0.00 xyz0 = 0.00 0.00 0.00 Gdiag_no -1 Reading surface /Applications/freesurfer/subjects/dados_Riba//fsaverage/surf/lh.white Done reading source surface INFO: reading qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh as MGH Done loading source values (nvtxs = 163842) INFO: mapping vertices to closest voxel INFO: resampling surface to volume INFO: sampled 73965 voxels in the volume INFO: writing output volume to teste_sig.mgz done And then, use tkmedit to view it: [Fernanda-Palhanos-Mac-Pro:freesurfer/subjects/dados_Riba] fernandapalhano% tkmedit fsaverage teste_sig.mgz mghRead(/Applications/freesurfer/subjects/dados_Riba//fsaverage/mri/teste_sig.mgz, -1): could not open file Error: Loading volume teste_sig.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Am I using wrong parameters in mri_surf2vol? Thanks again, Fernanda On Mon, Feb 21, 2011 at 5:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Fernanda if that's a surface overlay you'll need to sample it into the volume with mri_surf2vol cheers Bruce On Mon, 21 Feb 2011, Fernanda Palhano wrote: Hello, Does anyone knows if is it possible to overlay the surface file sig.mgh onto a T1 vol? I tried the command: tkmedit fsaverage T1.mgz -fthresh 2 -fmax 5 -overlay qdec/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh (where 2 and 5 were the thresholds I used in qdec), but it seems like I have only one point of the sig.mgh (in the slice 128) which is outside the volume. There's another way to do this? Thanks for the help! Fernanda 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
Re: [Freesurfer] mri_glmfit-sim doubt
It should be the case that the clusters in the 2.3 should be clusters in the 1.3, but there p-values will be different. It is possible that a cluster that is sig in the 2.3 is not sig in the 1.3, particularly small clusters like the two you have shown. Small clusters may be very likely at 1.3 under chance conditions. doug Rafa x wrote: Dear Freesurfers, I have performed a permutation test with the command: mri_glmfit-sim --glmdir rh.fsgd_subj_gauss005 --sim mc-z 1 THRESHOLD csd --sim-sign pos --seed 1297708255 And after that I have obtained the clusters with: mri_surfcluster --subject CNTRL_MCI_RAFA_average –mask rh.fsgd_subj_gauss005/mask.mgh --sum rh.fsgd_subj_gauss005/contrast/clustsum.txt --in rh.fsgd_subj_gauss005/contrast/sig.mgh --cwsig rh.fsgd_subj_gauss005/contrast/cwsig.mgh --vwsig rh.fsgd_subj_gauss005/contrast/vwsig.mgh --sign pos --csd rh.fsgd_subj_gauss005/csd/csd.j001-contrast.csd I’ve did it over the same dataset but with two different thresholds, THRESHOLD: 2.301 (pvalue=0.005) and 1.301 (pvalue=0.05). As far I know the cwsig.mgh resulting using the 1.3 threshold should be similar than the cwsig.mgh from the second thr, but with a more restrictive significative clusters (some coloured areas should disappear, in other words, clusters returned in the first case should be included in clusters returned by the 1.3 threshold). My results didn’t show that behaviour, some of the cwsig clusters can be contained in the other, but others don’t (see attached Figure). It is my reasoning correct? If so, why the images mismatching? Thank you all in advance. Rafa. ___ 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] question about weighted regression analysis
I assume that you are comparing maps of Version1:1v0 and Version2:2v0 ? I could imagine it going either way. If the true slope is 0 but the offset is non-0, then Version1 will give you an artificially high slope (and Verion2 will give you the correct slope at 0, and so no activation). Are you comparing this to a BV analysis? doug Katie Bettencourt wrote: So I created a weighted regression analysis to look at the effect of memory load in a particular brain region. Basically, I weighted the paradigms by a behavioral measure that reflected the number of items actually remembered (as set size was increased). As far as Doug told me there are basically 2 ways to weight your paradigm files. Version 1: Have 2 conditions, baseline (condition 0) and all the set sizes (condition 1). Condition 1 would then be weighted by the behavioral measure. Version 2: Have 3 conditions, baseline (condition 0), and then I represented each presentation as two different conditions, one with a weight that is always 1 (condition 1), the other weighted according to the behavioral measure (condition 2). The difference, as far as I understand it, in version 1, it is assumed that the response amplitude is ) when the weight is 0 (ie. that when you are attending to 0 items, brain activity = 0). Whereas, version 2, tests the slope of the HRF amplitude vs weight without the assumption above. However, I'm a bit confused as to the results I got. When I looked at the data from both versions, version 1 provided a much higher amount of activation and more areas activated than version 2. However, I believe version 2 better fits with the multiple regression analysis that is done in Brain Voyager. Can anyone give me a better explanation of what the difference between these analysis models is? Katie -- 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] Gammafit parameters
Yes, those are the default (from Dale and Buckner, ``Selective Averaging of Rapidly Presented Individual Trials Using fMRI,'' Human Brain Mapping, pp. 329-340, 1997.) doug Mandy Nagy wrote: Hi all, We are trying to use -gammafit when running the mkanalysis-sess command. In the FsFast Tutorial, the flag -gammafit 2.25 1.25 is used. Are those numbers the default? If not, what is the default? Thanks in advance. Best, Mandy Nagy ___ 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 doubt
This is not my understanding. It is completely dependent on the threshold used, which can be arbitrary. See Supplemental figure 7, page 16 of this document: http://www.jneurosci.org/cgi/data/30/6/2268/DC1/1 This was the motivation for Smith Nichols' TFCE: http://www.ncbi.nlm.nih.gov/pubmed/18501637 On 02/22/2011 05:53 AM, Rafa x wrote: Dear Freesurfers, I have performed a permutation test with the command: mri_glmfit-sim --glmdir rh.fsgd_subj_gauss005 --sim mc-z 1 THRESHOLD csd --sim-sign pos --seed 1297708255 And after that I have obtained the clusters with: mri_surfcluster --subject CNTRL_MCI_RAFA_average –mask rh.fsgd_subj_gauss005/mask.mgh --sum rh.fsgd_subj_gauss005/contrast/clustsum.txt --in rh.fsgd_subj_gauss005/contrast/sig.mgh --cwsig rh.fsgd_subj_gauss005/contrast/cwsig.mgh --vwsig rh.fsgd_subj_gauss005/contrast/vwsig.mgh --sign pos --csd rh.fsgd_subj_gauss005/csd/csd.j001-contrast.csd I’ve did it over the same dataset but with two different thresholds, THRESHOLD: 2.301 (pvalue=0.005) and 1.301 (pvalue=0.05). As far I know the cwsig.mgh resulting using the 1.3 threshold should be similar than the cwsig.mgh from the second thr, but with a more restrictive significative clusters (some coloured areas should disappear, in other words, clusters returned in the first case should be included in clusters returned by the 1.3 threshold). My results didn’t show that behaviour, some of the cwsig clusters can be contained in the other, but others don’t (see attached Figure). It is my reasoning correct? If so, why the images mismatching? Thank you all in advance. Rafa. ___ 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] retinotopy manual?
Hi Doug, When you say retinotopy 30, where 30 is the 30 second period. mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par Does period mean duration for a cycle or for the whole run? Thanks. Michelle ing Douglas N Greve gr...@nmr.mgh.harvard.edu: I don't have a formal manual yet (working on it). Below are a list of steps that you need to run. The version 5 retinotopy stream is now integrated with the rest of FSFAST, which is documented here: http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt doug 1. Create retinotopy paradigm file in each run directory, eg, session/bold/001/rtopy.par session/bold/002/rtopy.par etc This text file identifies the data in the directory in terms of the stimulus type (polar or eccen) and the direction (pos or neg). Its contents should look somethign like: stimtype polar direction pos 2. Run preprocessing preproc-sess -surface self lhrh -fwhm 5 3. Create analysis (30 sec period, 'rtopy.par' is the name of the paradigm file from above): mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ -retinotopy 30 -paradigm rtopy.par 4. Run analysis selxavg3-sess -a rtopy.self.lh -sf ... selxavg3-sess -a rtopy.self.rh -sf ... fieldsign-sess -a rtopy.self.lh -occip -sf ... fieldsign-sess -a rtopy.self.rh -occip -sf ... 5. View results a. Significance maps: tksurfer-sess -a rtopy.self.lh -s sessid b. Display raw angle tksurfer-sess -a rtopy.self.lh -s sessid -map angle c. Display angle masked by by sig tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked d. Display field sign tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign Michelle Umali wrote: Dear All, I was wondering if anyone knows of a step-by-step guide on how to do retinotopic analysis with freesurfer. 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 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] question about weighted regression analysis
You should also look at Version2:1v0. I bet a lot of the areas from Version1:1v0 will also show up. You can also create a Version3 in which you divide your presentations into a low-weight and a high-weight (but set the weight=1). Then create contrasts of low+high and high-low. The low+high should look like Version2:1v0 and the high-low should look like Version2:2v0. doug Katie Bettencourt wrote: Yes, those are the maps Ive been comparing. I've been comparing it to BV sort of, but that analysis is not surface based and Im not used to it, so I can't quite tell which is more accurate, though Version 2 gives a much smaller area of activity, which fits with the description of what I've been given about what to expect in BV. Attached is two pictures of the difference I get for Version 1:1v0 (labeled with single in the image name) and Version 2:2v0 (labeled with double in the name). As you can see, Version1 activates a much larger area than Version 2. I guess part of my problem is that I'm having trouble understanding exactly what these two versions are telling me about the data and what the differences is. Can you try to give me a sort of layman's explanation? Katie On Tue, Feb 22, 2011 at 11:45 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I assume that you are comparing maps of Version1:1v0 and Version2:2v0 ? I could imagine it going either way. If the true slope is 0 but the offset is non-0, then Version1 will give you an artificially high slope (and Verion2 will give you the correct slope at 0, and so no activation). Are you comparing this to a BV analysis? doug Katie Bettencourt wrote: So I created a weighted regression analysis to look at the effect of memory load in a particular brain region. Basically, I weighted the paradigms by a behavioral measure that reflected the number of items actually remembered (as set size was increased). As far as Doug told me there are basically 2 ways to weight your paradigm files. Version 1: Have 2 conditions, baseline (condition 0) and all the set sizes (condition 1). Condition 1 would then be weighted by the behavioral measure. Version 2: Have 3 conditions, baseline (condition 0), and then I represented each presentation as two different conditions, one with a weight that is always 1 (condition 1), the other weighted according to the behavioral measure (condition 2). The difference, as far as I understand it, in version 1, it is assumed that the response amplitude is ) when the weight is 0 (ie. that when you are attending to 0 items, brain activity = 0). Whereas, version 2, tests the slope of the HRF amplitude vs weight without the assumption above. However, I'm a bit confused as to the results I got. When I looked at the data from both versions, version 1 provided a much higher amount of activation and more areas activated than version 2. However, I believe version 2 better fits with the multiple regression analysis that is done in Brain Voyager. Can anyone give me a better explanation of what the difference between these analysis models is? Katie -- 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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. -- 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
Re: [Freesurfer] retinotopy manual?
For a cycle. So for the time it take the wedge to go all the way around or for the ring to start from center and return to center. doug Michelle Umali wrote: Hi Doug, When you say retinotopy 30, where 30 is the 30 second period. mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par Does period mean duration for a cycle or for the whole run? Thanks. Michelle ing Douglas N Greve gr...@nmr.mgh.harvard.edu: I don't have a formal manual yet (working on it). Below are a list of steps that you need to run. The version 5 retinotopy stream is now integrated with the rest of FSFAST, which is documented here: http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt doug 1. Create retinotopy paradigm file in each run directory, eg, session/bold/001/rtopy.par session/bold/002/rtopy.par etc This text file identifies the data in the directory in terms of the stimulus type (polar or eccen) and the direction (pos or neg). Its contents should look somethign like: stimtype polar direction pos 2. Run preprocessing preproc-sess -surface self lhrh -fwhm 5 3. Create analysis (30 sec period, 'rtopy.par' is the name of the paradigm file from above): mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ -retinotopy 30 -paradigm rtopy.par mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ -retinotopy 30 -paradigm rtopy.par 4. Run analysis selxavg3-sess -a rtopy.self.lh -sf ... selxavg3-sess -a rtopy.self.rh -sf ... fieldsign-sess -a rtopy.self.lh -occip -sf ... fieldsign-sess -a rtopy.self.rh -occip -sf ... 5. View results a. Significance maps: tksurfer-sess -a rtopy.self.lh -s sessid b. Display raw angle tksurfer-sess -a rtopy.self.lh -s sessid -map angle c. Display angle masked by by sig tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked d. Display field sign tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign Michelle Umali wrote: Dear All, I was wondering if anyone knows of a step-by-step guide on how to do retinotopic analysis with freesurfer. 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 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. -- 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
[Freesurfer] Converting an ascii file to a freesurfer volume file
Hello freesurfers, I am trying to convert a partially inflated surface .ply file created in afni to a freesurfer volume so that I can visualize the surfaces via tksurfer. Is there freesurfer command that converts text to volume, in essence the converse of mris_convert? And if not can you suggest a way that I can open the text file using a different graphical interface? Thank you in advance, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center UT Southwestern Medical Center The future of medicine, today. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all on data with anatomical abnormality or strong artifact
Hi, I run into the following error when running recon-all. ERROR: _FindFacePath: could not find path! in the process: Correcting Topology of defect 2 with euler number -9 (5 loops) computing statistics for defect 2: 1934 vertices location: [ (93,119,57) - average intensity = 85.136 ] The subject also has a huge anatomical abnormality or possibly an artifact ventral of the cerebellum (between cerebellum and pons). Brainmask.mgz also shows striping. When running the old topology fixer the following error occurs: mris_fix_topology: could not read brain volume from /mindhive/gablab/rhythm/cacophonix_July10/freesurfer_data/cacix7/mri/brain however, brain.mgz is there and loadable in tkmedit. Could the artifact be the reason for all this or is there another issue? Thanks for your help Eveline -- - Eveline Geiser PhD Massachusetts Institute of Technology Department of Brain and Cognitive Sciences phone: +617 324 63 71 e-mail: egei...@mit.edu http://web.mit.edu/gabrieli-lab/ ___ 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] recon-all on data with anatomical abnormality or strong artifact
Hi Eveline can you send us an image? What was your commandline for mris_fix_topology? I think you need to specify -mgz cheers Bruce On Tue, 22 Feb 2011, Eveline Geiser wrote: Hi, I run into the following error when running recon-all. ERROR: _FindFacePath: could not find path! in the process: Correcting Topology of defect 2 with euler number -9 (5 loops) computing statistics for defect 2: 1934 vertices location: [ (93,119,57) - average intensity = 85.136 ] The subject also has a huge anatomical abnormality or possibly an artifact ventral of the cerebellum (between cerebellum and pons). Brainmask.mgz also shows striping. When running the old topology fixer the following error occurs: mris_fix_topology: could not read brain volume from /mindhive/gablab/rhythm/cacophonix_July10/freesurfer_data/cacix7/mri/brain however, brain.mgz is there and loadable in tkmedit. Could the artifact be the reason for all this or is there another issue? Thanks for your help Eveline ___ 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] installation problem in ubuntu
try the command: sudo apt-get install tcl -- PPJ Please: cc the freesurfer list when answering 2011/2/22 Carolina Valencia cvalen...@linkdx.com.co Hi Pedro, Finally, I could install it with the license file and the environment is properly set without warnings. But trying to test it, following the instruction on the wiki page I have a problem cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit bert orig.mgz /usr/local/freesurfer/bin/tcl_setup: No existe el fichero o el directorio. in the .bashrc I copy the right location of the freesurfer folder FREESURFER_HOME=/home/cvalencia/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br run this command sudo rm -rf $FREESURFER_HOME 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Thanks Pedro, How I uninstall that version to re-install the correct version? I look for some answers and try rm -rf $FREESURFER_HOME It says that I don't have permission,how I can unistall it, if i'm the admin user? Thanks in advance, Carolina 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux Thanks, 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Please send the result of the command: uname -a On Mon, Feb 21, 2011 at 10:31, Carolina Valencia cvalen...@linkdx.com.co wrote: Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 I try to test it and it shows cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de ejecutable incorrecto. Binary file not executable. Thanks a lot, Carolina 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Jie, what hardware are you using? Is it a 64 bit operating system? cheers Bruce On Sat, 19 Feb 2011, Liukarl wrote: Hello, Freesurfer experts: I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and the only difference is that I installed it in my Documents, instead of local folder. Below is the output after “source $FREESURFER_HOME/SetUpFreeSurfer.sh” freesurfer-Linux-centos4-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/jie/Documents/freesurfer/ FSFAST_HOME /home/jie/Documents/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects MNI_DIR /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the freesurfer folder. But when I test it by “tkmedit bert orig.mgz”, it reponds “Illegal instruction” If I type in “recon-all”, it will show “ Required Arguments: -subjid subjid -process directive…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! Jie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient
Re: [Freesurfer] mkanalysis-sess says ERROR: bad format for seq.info file
Hi all,
Just for the record I comment that the problem was solved. It was the name
of the sequence, which containted the sting TR. This messed up the sanity
checks mkanalysis-sess. Thank you very much taking a look at it.
Best,
Pablo
On Fri, Feb 18, 2011 at 5:48 PM, Pablo Polosecki
ppolose...@mail.rockefeller.edu wrote:
Hi,
The full terminal output is pretty much what I sent previously:
Processing analysis: a1u
INFO: analysis a1u exists, but overwrite forced by user.
Setting TER to .1000
/home/ppolosecki/space/data/ppolosecki/cooked/2011/110211Quincy
ERROR: bad format for seq.info file,
/home/ppolosecki/space/data/ppolosecki/cooked/2011/110211Quincy
Is there a log file that the command spits out and I should send?
Best,
Pablo
On Fri, Feb 18, 2011 at 5:32 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
When I run this in version 4, it runs fine. Can you send me the full
terminal output?
Pablo Polosecki wrote:
Hi Doug,
Sure, here is the command line with all the variables replaced by their
actual values.
mkanalysis-sess \
-fsd bold \
-funcstem fmcus2 \
-analysis a1u \
-paradigm face_localizer_monkey.para \
-dt blocked \
-sf sf \
-df df \
-force \
-inorm \
-timewindow 40 \
-polyfit 2 \
-TR 2. \
-gammafit 0 1.25 \
-gammaexp 2 \
-nconditions 7 \
-runlistfile rlf1 \
-mask brain_fmcu \
-taumax 20 \
-acfbins 1 \
-fix-acf \
-noautostimdur \
-motioncor -mcextreg
Thanks again,
Pablo
On Fri, Feb 18, 2011 at 12:33 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
Can you send the actual command without any variables? thanks
doug
Pablo Polosecki wrote:
Hi,
The command line it's within the attached script, so it might
not look as informative whn looked at on its own. However it is:
mkanalysis-sess \
-fsd bold \
-funcstem $funcstem \
-analysis $analysis \
-paradigm $paradigm \
-dt blocked \
-sf sf \
-df df \
-force $tpef_string \
-inorm \
-timewindow ${timewindow} \
-polyfit 2 \
-TR $TR ${TER_string}\
-gammafit $gammafit \
-gammaexp $gammaexp \
-nconditions $nconditions \
-runlistfile $runlistfile \
-mask ${mask_stem} \
-taumax $taumax \
-acfbins 1 \
-fix-acf \
-noautostimdur \
-motioncor -mcextreg
On Fri, Feb 18, 2011 at 11:57 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
What is your command-line?
Pablo Polosecki wrote:
Hi,
I forgot to put the version, my bad. The version is 4.5.
Thanks,
Pablo
On Fri, Feb 18, 2011 at 11:21 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
which version are you using? The seq.info
http://seq.info http://seq.info
http://seq.info file
has not been used in a long time.
doug
Pablo Polosecki wrote:
Hi all,
I am trying to define an analysis for a block-based
functional
scan using mkanalysis-sess.
When I run it, I get the following output with
an error
message:
Setting TER to .1000
/home/ppolosecki/space/data/ppolosecki/cooked/2011/110211Quincy
ERROR: bad format for seq.info http://seq.info
http://seq.info
http://seq.info
http://seq.info file,
/home/ppolosecki/space/data/ppolosecki/cooked/2011/110211Quincy
The seq.info http://seq.info http://seq.info
http://seq.info
http://seq.info file
(attached) was produced by the unpacksdcmdir
command and it
looks no different from other ones I have seen. The
information there seems correct to me.
Could someone perhaps point out possible reasons
why this
could happen? The script I use to call
mkanalysis-sess
containing all the parameters used is attached.
Thank you
