Re: [Freesurfer] Cortical gray matter surface area
Thanks Andreia, this does appear to have worked. Please forgive my ignorance but I do just want to double check two things; 1) The first commands you have given provide the stats for the two hemispheres of the cerebral cortex only based on the pial surface, whereas the second set of commands provide the pial boundary stats for the whole brain rather than just cortex? 2) The surface area value that I am looking for (grey matter surface area at the grey/pial boundary) is listed in the new stats table next to: *# Measure Cortex, WhiteSurfArea, White Surface Total Area,* ? Thanks again, Will On Tue, Sep 9, 2014 at 5:36 PM, will brown willbrown1...@gmail.com wrote: Thanks very much Andreia, yes this does look like what I want. I haven't had a chance to test it yet but it does indeed appear to answer my question. Thanks to those that have offered answers, to clarify, I did indeed mean the surface area of the pial surface rather than the white/grey boundary. Will On Wed, Sep 3, 2014 at 1:12 AM, _andre...@sapo.pt wrote: Hi Will, I use the following commands to get surface area from the pial surface: In the subject label dir: mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.*aparc.pial*.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.*aparc.pial*.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab SUBJ rh pial Then run aparcstats2table using *aparc.pial* instead of aparc (only because I called this new parcellation aparc.pial) To get the total surface area of each hemisphere I use: In the subject stats dir: mris_anatomical_stats -l ../label/lh.cortex.label -f lh.*total_pial*.stats -b SUBJ lh pial mris_anatomical_stats -l ../label/rh.cortex.label -f rh.*total_pial*.stats -b SUBJ rh pial Then run aparcstats2table using *total_pial* instead of aparc (again, only because I called this new parcellation total_pial. You may call it whatever you'd like) Just remeber to leave the specified dirs when creating the tables. If you dont't I think they will be created in the current dir. I use FS 5.0. Is this what you want? Best, Andreia Citando will brown willbrown1...@gmail.com: Hi all, I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info. ?.aparc.stats reports: Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2 How about the gray matter? Thanks, Will ___ 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] hippocampal subfields: from posterior to binary masks
Dear Eugenio, /assign to each voxel the label with the highest posterior probability /implies that each voxel must belong to *one and only one* label, right? I've found that this is not the case with the posterior_*.mgz files outputted by freesurfer, where each voxel (especially the ones with the lower prob values) can belong to multiple labels. The passages I've done to come up at this conclusion was: 1) binarize all the posterior maps 2) summing them up 3) search for values greater than 1 4) if there are values 1, then there are voxels belonging to multiple labels. I've found voxels belonging to 7 different labels at the same time! I think that the posterior files outputted by freesurfer are missing the final step of required to each voxel to the *single* label with the highest posterior prob. I think that a clarification from the developers is needed here. Best regards, Luigi. ___ 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] hippocampal subfields: from posterior to binary masks
Hi again, Luigi, this sentence that you wrote summarizes everything pretty well: I think that the posterior files outputted by freesurfer are missing the final step of required to each voxel to the single label with the highest posterior prob. We will implement this in the next FS release. Regarding how the discrete labels are computed: For each voxel, one would look at all the posterior probabilities, and assign the label corresponding to the largest posterior. There is a small chance that there is a tie between 2 (or more) classes; in that case, you can pick between those classes at random. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Luigi Antelmi luigi.ante...@gmail.com To: e iglesias e.igles...@bcbl.eu, freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 9, 2014 11:48:10 AM Subject: Re: [Freesurfer] hippocampal subfields: from posterior to binary masks Dear Eugenio, assign to each voxel the label with the highest posterior probability implies that each voxel must belong to one and only one label, right? I've found that this is not the case with the posterior_*.mgz files outputted by freesurfer, where each voxel (especially the ones with the lower prob values) can belong to multiple labels. The passages I've done to come up at this conclusion was: 1) binarize all the posterior maps 2) summing them up 3) search for values greater than 1 4) if there are values 1, then there are voxels belonging to multiple labels. I've found voxels belonging to 7 different labels at the same time! I think that the posterior files outputted by freesurfer are missing the final step of required to each voxel to the single label with the highest posterior prob. I think that a clarification from the developers is needed here. Best regards, Luigi. ___ 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] hippocampal subfields: from posterior to binary masks
Ok Eugenio, I just have a final consideration. Whenever this last step will be implemented, there will still will be the problem of how to binarize those subfields in a way that makes sense. Plese correct me if I'm wrong: given that at the end counting all the non-zero voxels will always overestimate the volume calculated with kvlQuantifyPosteriorProbabilityImages, one must further threshold the posteriors to make the two measures consistent with each other. Right? Best, Luigi. in order to make the result consistent with the volume calculated by kvlQuantifyPosteriorProbabilityImages, 2014-09-09 11:58 GMT+02:00 Eugenio Iglesias e.igles...@bcbl.eu: Hi again, Luigi, this sentence that you wrote summarizes everything pretty well: I think that the posterior files outputted by freesurfer are missing the final step of required to each voxel to the single label with the highest posterior prob. We will implement this in the next FS release. Regarding how the discrete labels are computed: For each voxel, one would look at all the posterior probabilities, and assign the label corresponding to the largest posterior. There is a small chance that there is a tie between 2 (or more) classes; in that case, you can pick between those classes at random. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Luigi Antelmi luigi.ante...@gmail.com To: e iglesias e.igles...@bcbl.eu, freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, September 9, 2014 11:48:10 AM Subject: Re: [Freesurfer] hippocampal subfields: from posterior to binary masks Dear Eugenio, assign to each voxel the label with the highest posterior probability implies that each voxel must belong to one and only one label, right? I've found that this is not the case with the posterior_*.mgz files outputted by freesurfer, where each voxel (especially the ones with the lower prob values) can belong to multiple labels. The passages I've done to come up at this conclusion was: 1) binarize all the posterior maps 2) summing them up 3) search for values greater than 1 4) if there are values 1, then there are voxels belonging to multiple labels. I've found voxels belonging to 7 different labels at the same time! I think that the posterior files outputted by freesurfer are missing the final step of required to each voxel to the single label with the highest posterior prob. I think that a clarification from the developers is needed here. Best regards, Luigi. ___ 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] Cortical gray matter surface area
Hi Will, Just to clarify, what version of FS are you using? I think it might not be 5.0 and I don't know if everything aplies if we are using different versions. 1) Yes, it is only based on the pial surface (and these command lines are for the aparc, DK altas). The second set provides the surface area for each hemisphere without including, for example, the pial surface that you see in the hippocampus which is not accurate and one should not care about. In the end, the second set gives you the sum of the areas in aparc, thus, you can just make a sum of that parcellation if you want. I just realized that. 2) No. In the new stats file, the value that you want is at the bottom: # ColHeaders StructName NumVert SURFAREA GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd And when running aparcstats2table that's the value you should get in the table. I think that # MEASURE CORTEX, WHITESURFAREA, WHITE SURFACE TOTAL AREA may be including more stuff since it is bigger. If what you want is only the total hemisphere surface area you only need to run the second set of commands. If you want the area of each DK altas parcellation then run the first set and then simply add them to get total hemisphere surface area. Someone from Freesurfer staff will correct me if I'm wrong. (Please) I'm Ccing Doug since he was replying to your previous emails. Let's wait for their feedback. Andreia Citando will brown willbrown1...@gmail.com: Thanks Andreia, this does appear to have worked. Please forgive my ignorance but I do just want to double check two things; 1) The first commands you have given provide the stats for the two hemispheres of the cerebral cortex only based on the pial surface, whereas the second set of commands provide the pial boundary stats for the whole brain rather than just cortex? 2) The surface area value that I am looking for (grey matter surface area at the grey/pial boundary) is listed in the new stats table next to: # MEASURE CORTEX, WHITESURFAREA, WHITE SURFACE TOTAL AREA, ? Thanks again, Will On Tue, Sep 9, 2014 at 5:36 PM, will brown willbrown1...@gmail.com wrote: Thanks very much Andreia, yes this does look like what I want. I haven't had a chance to test it yet but it does indeed appear to answer my question. Thanks to those that have offered answers, to clarify, I did indeed mean the surface area of the pial surface rather than the white/grey boundary. Will On Wed, Sep 3, 2014 at 1:12 AM, _andre...@sapo.pt wrote: _Hi Will, I use the following commands to get surface area from the pial surface: In the subject label dir:_ _mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.APARC.PIAL.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial_ _mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.APARC.PIAL.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab SUBJ rh pial _ _Then run aparcstats2table using APARC.PIAL instead of aparc (only because I called this new parcellation aparc.pial) To get the total surface area of each hemisphere I use: In the subject stats dir:_ _mris_anatomical_stats -l ../label/lh.cortex.label -f lh.TOTAL_PIAL.stats -b SUBJ lh pial_ _mris_anatomical_stats -l ../label/rh.cortex.label -f rh.TOTAL_PIAL.stats -b SUBJ rh pial_ _Then run aparcstats2table using TOTAL_PIAL instead of aparc (again, only because I called this new parcellation total_pial. You may call it whatever you'd like)_ _Just remeber to leave the specified dirs when creating the tables. If you dont't I think they will be created in the current dir. I use FS 5.0. Is this what you want? Best, Andreia_ _Citando will brown willbrown1...@gmail.com:_ _Hi all, _ _ _ _I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info._ _ _ _?.aparc.stats reports:_ _ _ _Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2_ _ _ _How about the gray matter?_ _ _ _Thanks,_ _Will_ _ _ _ _ _ _ ___ 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
[Freesurfer] how to shrink wm surface
Dear Freesurfers, After running recon-all, the wm surfaces are too close to the pial surface, some gray matter is segmented as white matter as seen in the attached picture (red cross: a bigger cortical part is included in the white matter). How can I shrink the wm surface? Thank you for your help! Andrea ___ 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 shrink wm surface
mris_expand may do what you want. You can use it to shrink or expand the points on a surface by a fixed percentage or a fixed distance. Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Andrea Horváth Sent: Tuesday, September 09, 2014 7:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] how to shrink wm surface Dear Freesurfers, After running recon-all, the wm surfaces are too close to the pial surface, some gray matter is segmented as white matter as seen in the attached picture (red cross: a bigger cortical part is included in the white matter). How can I shrink the wm surface? Thank you for your help! Andrea ___ 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] freesurfer commands from MATLAB
Dear Freesurfers,
Is there a way of calling freesurfer-scripts from within MATLAB?
I know there are some setups needed to make MATLAB understand where it can
find the commands (I have done this before with FSL).
I am using bash, and when I type the Freesurfer commands in a terminal by
hand, they work. So I am guessing it must have to do with setting up the
environment:
freesurf_path ='Applications/freesurfer';
setenv('FREESURFDIR',freesurf_path)
setenv('FREESURFOUTPUTTYPE','NIFTI_GZ')
curpath = getenv('PATH');
setenv('PATH',sprintf('%s:%s',fullfile(freesurf_path,'bin'),curpath));
Thanks a lot for any help,
Barbara
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Re: [Freesurfer] freesurfer commands from MATLAB
Hi Barbara,
You haven't told us which OS you use.
For example in Mac OS it is necessary to start up MATLAB by typing matlab
into the X11 terminal, otherwise the system OS will not recognize the
commands given via matlab (e.g. system('mycommand') .)
Best,
Markus
2014-09-09 13:45 GMT+02:00 Barbara Kreilkamp bakk@googlemail.com:
Dear Freesurfers,
Is there a way of calling freesurfer-scripts from within MATLAB?
I know there are some setups needed to make MATLAB understand where it can
find the commands (I have done this before with FSL).
I am using bash, and when I type the Freesurfer commands in a terminal by
hand, they work. So I am guessing it must have to do with setting up the
environment:
freesurf_path ='Applications/freesurfer';
setenv('FREESURFDIR',freesurf_path)
setenv('FREESURFOUTPUTTYPE','NIFTI_GZ')
curpath = getenv('PATH');
setenv('PATH',sprintf('%s:%s',fullfile(freesurf_path,'bin'),curpath));
Thanks a lot for any help,
Barbara
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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
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error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.
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Re: [Freesurfer] Help with pial boundary
Hi Joann it looks like some white matter is not being identified in the ?h.white surface. You need to diagnose why this is happening. It's probably an inaccurately corrected topological defect. Have you gone through the tutorials? You will likely need to add some wm voxels back in. If you upload the subject we'll take look if you like. cheers Bruce On Tue, 9 Sep 2014, Joann Poh wrote: Dear All, I'm having issues with the pial surface - temporal lobe is being under-estimated (see wm-pial.png) where the red cross is. (Frontal lobe also has similar issues.) In wm.mgz, the white matter looks fine, as well as in aseg.mgz (see aseg-wm-pial.png) but just not the pial boundary. What can I do to rectify this? On a side note, I've tried adding control points (to the frontal lobe to solve a similar problem) but the pial boundary still does not cover the gray matter and I'm missing bits. Thank you. Kind regards, Joann ___ 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 shrink wm surface
Hi Andrea what is the background image? This is usually either a failure of the intensity normalization or of the surface deformation/segmentation to adaptively estimate the underlying intensity distributions of the gray/white matter. If you look in recon-all.log for that subject you will find a set of lines like: setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 59.1 (was 40) setting MAX_GRAY to 100.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 47.2 (was 40) in your case for example you will probably find that the min_border_white is too high or tha the max_gray is too low. You can set these using the expert opts for both mri_segment and mris_make_surfaces. cheers Bruce On Tue, 9 Sep 2014, Andrea Horváth wrote: Dear Freesurfers, After running recon-all, the wm surfaces are too close to the pial surface, some gray matter is segmented as white matter as seen in the attached picture (red cross: a bigger cortical part is included in the white matter). How can I shrink the wm surface? Thank you for your help! Andrea ___ 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] Tracula reconstructed tracts quality
Hi Anastasia, Thanks for taking a look and point that out. I'll have to be more careful in checking the source images, instead of going by the notes (and memory of events years past) left by the previous engineers on the project.;) -Peggy On Mon, Sep 8, 2014 at 6:21 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Peggy - I looked at the data. Unfortunately, the voxel size is 0.9x0.9x4 in the first time point and 0.9x0.9x5.2 in the second. So not only is the resolution extremely anisotropic, which is problematic for tractography, but it's also different between scans, which almost guarantees that you will find longitudinal changes (except you won't know if it's because the brain is changing or the scan is changing). Finally, the 12 directions that you have may not be sufficient to fit a crossing-fiber model like the ball-and-stick model, which may explain the noisy output. a.y On Mon, 8 Sep 2014, Peggy Skelly wrote: Hello Tracula experts, I was wondering if you could comment on the quality of the tracts reconstructed with our 1.5T data. These 2 files are from the same subject at 2 timepoints, processed in the longitudinal stream. Is much of the non-smooth look of the tracts due to the resolution of the dwi scans (1.8x1.8x4mm)? What could be the source of the diagonal lines/gaps in the tracts seen in tp1 when viewed from above? Thanks, Peggy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Syntax Error: trac-all -bedp
Dear Anastasia, Barbara FS-community, The preprocessing step of Tracula was succesfully completed. However when I try to do the next step: fitting the Ball Stick model I get another error: mri@ge24c165:/media/mri/DATAPART11/ROBBY/FREESURFER$ trac-all -bedp -c dmrirc.info INFO: SUBJECTS_DIR is /media/mri/DATAPART11/ROBBY/FREESURFER/T1 INFO: Diffusion root is /media/mri/DATAPART11/ROBBY/FREESURFER/T1 Actual FREESURFER_HOME /usr/local/freesurfer INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /apps/gent/SL6/sandybridge/software/FreeSurfer/5.3.0-centos4_x86_64 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /media/mri/DATAPART11/ROBBY/FREESURFER/T1/INP_080_LISA_V_1/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected I have already searched through your mailing list and found a topic where the same problem is discussed:[Freesurfer] FreeSurfer 5.2 TRACULA and FSL 5. I've already checked for the things that were suggested here, but I didn't find a solution. Hoping for some help? Thanks, Regards, Robby ___ 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] QCACHE error
Dear list, I'm running longitudinal two stage model as is described in the tutorial here: http://freesurfer.net/fswiki/LongitudinalTwoStageModel First, I've proceeded with longitudinal pipeline all my data, second, I've created longitudinal qdec table, and then, I've started to qcache my data, which after few seconds ends up with error: SUBJECT template_malfara fwhm 0 computing PC1 mris_calc -o /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/template_malfara/surf/lh.long.thickness-pc1.fwhm0.mgh ./tmp-template_malfara_lh_thickness_Dkx9j1/beta1.mgh div ./tmp-template_malfara_lh_thickness_Dkx9j1/tp1.mgh Saving result to '/home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/template_malfara/surf/lh.long.thickness-pc1.fwhm0.mgh' (type = MGH ) [ ok ] ERROR 1 : mris_calc compute percent change (pc1) problem? Please, could you give me a hint how I can overcome this error? -- Gayane Aghakhanyan, MD PhD candidate, Institute of Life Sciences Scuola Superiore Sant'Anna Piazza Martiri della Libertà Pisa 56127, Italy tel: +39 327 7013870 email: g.aghakhan...@sssup.it ___ 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] QCACHE error
Hi Gayane, what happens if you run the mris_calc command directly? Also check if all the inputs really exist. It could be that you need to update mris_calc there was a problem with long file names in an earlier version. Which FS version are you using? Best, Martin On 09/09/2014 09:51 AM, Gayane Aghakhanyan wrote: Dear list, I'm running longitudinal two stage model as is described in the tutorial here: http://freesurfer.net/fswiki/LongitudinalTwoStageModel First, I've proceeded with longitudinal pipeline all my data, second, I've created longitudinal qdec table, and then, I've started to qcache my data, which after few seconds ends up with error: SUBJECT template_malfara fwhm 0 computing PC1 mris_calc -o /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/template_malfara/surf/lh.long.thickness-pc1.fwhm0.mgh ./tmp-template_malfara_lh_thickness_Dkx9j1/beta1.mgh div ./tmp-template_malfara_lh_thickness_Dkx9j1/tp1.mgh Saving result to '/home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/template_malfara/surf/lh.long.thickness-pc1.fwhm0.mgh' (type = MGH ) [ ok ] ERROR 1 : mris_calc compute percent change (pc1) problem? Please, could you give me a hint how I can overcome this error? -- Gayane Aghakhanyan, MD PhD candidate, Institute of Life Sciences Scuola Superiore Sant'Anna Piazza Martiri della Libertà Pisa 56127, Italy tel: +39 327 7013870 email: g.aghakhan...@sssup.it mailto:g.aghakhan...@sssup.it ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology 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] freesurfer commands from MATLAB
Hi Markus,
Thank you for this, yes I am running Mac OS 10.9.2, and the freesurfer
command freeview loads the data fine when I start up matlab from the bash
terminal (even without using XQuartz, my equivalent of X11) and call this
command.
Thanks for the quick help!
Barbara
On Tue, Sep 9, 2014 at 12:59 PM, Markus Gschwind markus.gschw...@gmail.com
wrote:
Hi Barbara,
You haven't told us which OS you use.
For example in Mac OS it is necessary to start up MATLAB by typing matlab
into the X11 terminal, otherwise the system OS will not recognize the
commands given via matlab (e.g. system('mycommand') .)
Best,
Markus
2014-09-09 13:45 GMT+02:00 Barbara Kreilkamp bakk@googlemail.com:
Dear Freesurfers,
Is there a way of calling freesurfer-scripts from within MATLAB?
I know there are some setups needed to make MATLAB understand where it
can find the commands (I have done this before with FSL).
I am using bash, and when I type the Freesurfer commands in a terminal by
hand, they work. So I am guessing it must have to do with setting up the
environment:
freesurf_path ='Applications/freesurfer';
setenv('FREESURFDIR',freesurf_path)
setenv('FREESURFOUTPUTTYPE','NIFTI_GZ')
curpath = getenv('PATH');
setenv('PATH',sprintf('%s:%s',fullfile(freesurf_path,'bin'),curpath));
Thanks a lot for any help,
Barbara
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[Freesurfer] mri_convert
Dear FreeSurfer experts, I get a new message when I use mri_convert command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file, and goes to infinite loop. *mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz* mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards, Nooshin ___ 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] Using fieldmap to correct EPI distortions
the commands I gave you will do this On 09/06/2014 07:47 AM, Reza Rajimehr wrote: I forgot to mention that I want to use undistorted EPI volumes for the functional-anatomical registration. Hi, I have a basic question, but the answer can be useful for others as well. I am doing a customized preprocessing of monkey functional data in FS-FAST v5.3. After motion correction and before functional-anatomical registration, I want to use fieldmap data to correct spatial distortions of EPI data. So: My fieldmap data: dicom files from a fieldmap scan (there are actually two series of dicom files for that scan) My EPI data: fmc.nii.gz files in run folders Now I have three questions: 1) How can I unpack the fieldmap data? An example command ... 2) How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an example command would be very useful. 3) How will the undistorted volumes be used later on in the FS-FAST analysis stream? Your help would be very much appreciated. Thanks, Reza ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Using fieldmap to correct EPI distortions
On 09/06/2014 07:10 AM, Reza Rajimehr wrote: Hi, I have a basic question, but the answer can be useful for others as well. I am doing a customized preprocessing of monkey functional data in FS-FAST v5.3. After motion correction and before functional-anatomical registration, I want to use fieldmap data to correct spatial distortions of EPI data. So: My fieldmap data: dicom files from a fieldmap scan (there are actually two series of dicom files for that scan) My EPI data: fmc.nii.gz files in run folders Now I have three questions: 1) How can I unpack the fieldmap data? An example command ... I think you get two series out, one magnitude and one phase, just convert those to nifti 2) How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an example command would be very useful. something like epidewarp.fsl --mag mag.nii --dph phase.nii --exf template.nii --o b0dc.nii ... You have to add --tediff and --esp, but those depend on you sequence Put the output (b0dc.nii) into session/bold (or session/rest, or where ever your fmri data are located) 3) How will the undistorted volumes be used later on in the FS-FAST analysis stream? When you run preproc-sess and mkanalysis-sess add -b0dc to the command line Your help would be very much appreciated. Thanks, Reza ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] how to interpret a change in area of 0.004 mm² per year?
This is tough to interpret, but basically, yes it would be 0-.004mm2/year. It is not quite right to say that it is at that vertex because of smoothing, but in that area. It is also hard to say what the total change would be for a cluster. One could sum the changes over the cluster vertices, but that would probably over-estimate the change. doug On 09/06/2014 09:51 AM, Lars M. Rimol wrote: Hi, I have performed a longitudinal analysis using the lme module in FreeSurfer, with this model: *intercept(random effect) + centered age + group + group x centered age + sex* I tested the effect of time with this contrast vector [ 0 1 0 0 0 ]. Dependent variable is area. Here, mapping the second beta means mapping the effect size for (change over) time. In the beta map, I find values from 0 to 0.004. I would interpret that to mean that local area shrinks by at most 0.004 mm² per year in the reference group. But I'm not 100% sure about the biological (or geometrical) meaning of that. Can I interpret this literally as the mean yearly shrinkage of the three triangles surrounding a given vertex, the average of whose area comprises the area score of the vertex, being 4/1000 mm? Of course, these maps are smoothed with 30mm, so the real spatial resolution is nowhere near this Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] within individual multimodal correlation
Why do you have your activation in a .w file? If you can save it as
.mgh, then things get a lot easier. You can convert it to mgh using
mri_surf2surf. You'll need to convert the thickness to mgh with
mri_convert lh.thickness lh.thickness.mgh. Then load the two mgh files
into matlab, eg,
thick = MRIread('lh.thickness.mgh');
fmri = MRIread('yourfmri.mgh');
thick and fmri will be structures where the .vol element is the data you
want
On 09/08/2014 10:00 AM, lorenzo pasquini wrote:
Dear Freesurfers,
I am currently investigating the relationship between functional
activation and cortical thickness at a within-subject vertex-based
level. For this purpose I have mapped my activation on the vertex
surface in the same subject. As you can see from the attached
screenshot, I am able to visualize for the same vertex (e.g.
coordinates vertex normal [0.97 -0.17 -0.14], curvature -0.190746) the
value of the individual activation map (3.002379 on TkSurfer) and the
individual cortical thickness value (2.61282 on FreeView).
What I need, is for every vertex in my surface the activation value
and the correspondent cortical thickness value to be able to compute a
vertex-based individual correlation of both modalities.
How ca I extract this information from my data? The activation map is
saved in .w (paint format)... is it possible to extract such a matrix
by saving my data in an other format? I have been trying
read_annotation and other matlab commands as read_surf but could not
access a matrix of vertex specific thickness/activation values. Is
there a more elegant way to compute an individual correlation/general
linear model in freesurfer (please note that the analysis in WITHIN a
subject)? Or should I use softwares as SurfStat
(http://www.math.mcgill.ca/keith/surfstat/)?
Any help would be very appreciated, thanks,
Lorenzo
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Re: [Freesurfer] mri_glmfit problem
That means that you need to add something like --surface fsaverage lh the above assumes that you used the left hemi of fsaverage On 09/05/2014 02:56 AM, Minjeong Wang wrote: Dear all, i have some problem with mri_glmfit. The error message is you must use '--surface subject hemi' with surface data What do I do for solving this problem?? Help me.. :( M.J. - mri_glmfit \ --glmdir lh.cdr.glmdir \ --y lh.cdr.thickness.10.mgh \ --fsgd cdr.fsgd dods \ --C normal-CDR0.5.mtx \ --C normal-CDR1.mtx \ --C CDR0.5-CDR1.mtx \ --C group.effect.mtx \ --C normal+CDR0.5-vs-CDR1.mtx \ --surf fsaverage lh \ --cortex \? --glmdir lh.cdr.glmdir \ ? --y lh.cdr.thickness.10.mgh \ ? --fsgd cdr.fsgd dods \ ? --C normal-CDR0.5.mtx \ ? --C normal-CDR1.mtx \ gdfReadHeader: reading cdr.fsgd INFO: gd2mtx_method is dods $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Applications/freesurfer/subjects cmdline mri_glmfit --glmdir lh.cdr.glmdir --y lh.cdr.thickness.10.mgh --fsgd cdr.fsgd dods --C normal-CDR0.5.mtx --C normal-CDR1.mtx sysname Darwin hostname Youngui-Mac-Pro.local machine x86_64 user younghopark FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/lh.cdr.thickness.10.mgh logyflag 0 usedti 0 FSGD cdr.fsgd glmdir lh.cdr.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.cdr.glmdir Loading y from /Applications/freesurfer/subjects/lh.cdr.thickness.10.mgh ERROR: you must use '--surface subject hemi' with surface data [Youngui-Mac-Pro:/Applications/freesurfer/subjects] younghopark% --C CDR0.5-CDR1.mtx \ --C: Command not found. [Youngui-Mac-Pro:/Applications/freesurfer/subjects] younghopark% --C group.effect.mtx \ --C: Command not found. [Youngui-Mac-Pro:/Applications/freesurfer/subjects] younghopark% --C normal+CDR0.5-vs-CDR1.mtx \ ? --surf fsaverage lh \ ? --cortex \ ? --C: Command not found. ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] From bedpostX and recon-all to tracula
Can you please attach the trac-all.log file, which has the entire output from beginning to end? Ofter something goes wrong earlier that causes the program to fail later in the process. Also, we'll need your original configuration file. Thanks! On Mon, 8 Sep 2014, Katherine Damme wrote: Hello Freesurfer Community! Thank you Anastasia and Christopher, I am still getting ending with errors and the log file gives no clue that I have been able to detect, see attached. Any help would be appreciated! On Thu, Sep 4, 2014 at 4:29 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Kate - There is an example configuration file for tracula in your freesurfer distribution ($FREESURFER_HOME/bin/dmrirc.example). The same file is also here: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc If you attach your configuration file and the log file (scripts/trac-all.log), we can try to troubleshoot. a.y On Wed, 3 Sep 2014, Katherine Damme wrote: Hello Freesurfer Community! I have sucessfully completed diffusion preprocessing in FSL and the recon-all of the structural image and would like to use tracula for the tract reconstruction. I keep having trouble with my configuration file. Does anyone have a bedpostX tracula config file they could share as an example?H Thank you! Kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Error in creating stats using tracula
Hi Neeraj - The libnetcdf error you're getting probably means that you should install a different build of freesurfer (centos 4 instead of centos 6). Which one are you currently using? In the future please email the freesurfer list instead of me personally with questions about tracula. The purpose of the list is to get the messages archived so that people can search for questions that have been answered before in the archives. Thanks! a.y On Tue, 9 Sep 2014, Neeraj Upadhyay wrote: Dear Anastasia Yendiki, While analysing the DTI data with Tracula ,I stuck to a problem which is attached in the screen shot .Please guide me how to solve it because this is the step to analyse the data group wise using voxelwise diffusion measures. hope for a positive reply soon. With warm Regrads -- Neeraj upadhyay PhD Fellow Department of Neurology and Psychiatry University of Rome La' Sapienza Viale della Universita 30-00185,Rome,Italy Guide: Professor Alfredo Berardelli contact no:+393735282419 ___ 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] Syntax Error: trac-all -bedp
Hi Robby - Since you're running it locally and not on a cluster, you can just run bedpostx directly: bedpostx /media/mri/DATAPART11/ROBBY/FREESURFER/T1/INP_080_LISA_V_1/dmri a.y On Tue, 9 Sep 2014, Robby De Pauw wrote: Dear Anastasia, Barbara FS-community, The preprocessing step of Tracula was succesfully completed. However when I try to do the next step: fitting the Ball Stick model I get another error: mri@ge24c165:/media/mri/DATAPART11/ROBBY/FREESURFER$ trac-all -bedp -c dmrirc.info INFO: SUBJECTS_DIR is /media/mri/DATAPART11/ROBBY/FREESURFER/T1 INFO: Diffusion root is /media/mri/DATAPART11/ROBBY/FREESURFER/T1 Actual FREESURFER_HOME /usr/local/freesurfer INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /apps/gent/SL6/sandybridge/software/FreeSurfer/5.3.0-centos4_x86_64 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /media/mri/DATAPART11/ROBBY/FREESURFER/T1/INP_080_LISA_V_1/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected I have already searched through your mailing list and found a topic where the same problem is discussed:[Freesurfer] FreeSurfer 5.2 TRACULA and FSL 5. I've already checked for the things that were suggested here, but I didn't find a solution. Hoping for some help? Thanks, Regards, Robby ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_convert
Hi Nooshin does it just hang there? How long do you let it run? Bruce On Tue, 9 Sep 2014, Nooshin Zadeh wrote: Dear FreeSurfer experts, I get a new message when I use mri_convert command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file, and goes to infinite loop. mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards, Nooshin ___ 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] FW: Most recent/complete FreeSurfer + Patches?
Hi guys! We would like to install the latest and greatest FreeSurfer on the processing cluster used by the CNDA at Washington University. We're thinking about installing the 5.3.0-HCP, and then over that, the released 5.3.0 patches. We're looking for verification that doing the install this way makes sense and that these two code sets don't conflict in any way. We know that the 5.3.0-HCP version updates the mris_make_surfaces, however, the patches do not include that update, which is why we are thinking about starting with 5.3.0-HCP as the base install. Note that this is being done on CentOS 6.x The currently available patches seem to include: mni152reg mri_mcsim mri_segstats recon-all tksurfer-sess tksurferfv Is that a complete list or did we miss some binaries/scripts? Also, it seems that the 'patch' binaries are dynamically linked, while the release binaries are statically linked. Besides dependency issues, could this cause an issue with results consistency, etc. if other system libraries get updated? Thanks, guys. Hope all is well. Matt House, Jenny Gurney and John Flavin @WU in STL The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_convert
Yes. It just hang there. I even let it run for few days! and no outcome. On Sep 9, 2014 12:19 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Nooshin does it just hang there? How long do you let it run? Bruce On Tue, 9 Sep 2014, Nooshin Zadeh wrote: Dear FreeSurfer experts, I get a new message when I use mri_convert command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file, and goes to infinite loop. mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards, Nooshin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh
Hi Doug, Thanks for your reply. I can certainly test it. Could you tell me how I can run this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' that I use is under '/usr/local/freesurfer/stable5_0_0/bin/' Best, Hamdi From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, September 08, 2014 11:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh That was an oversight. I've attached a version that should work. Can you test it for me? Once I know it works I'll check it in to tree. doug On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote: Dear FS experts, I have a question about a MC output file. When I run the MC sim (using mri_glmfit-sim) on the surface, it generates a bunch of files including a 'sig.masked.mgh', which is nice for displaying the significance map limited to the clusters that survive the MC correction. However, when I run it on the volume, it doesn't generate this specific file. Does anyone know the reason for that? Is there an alternative way to display the significance map that show only the clusters that survive the MC correction? Many thanks! Hamdi -- Hamdi Eryilmaz, PhD Massachusetts General Hospital A.A. Martinos Center for Biomedical Imaging Psychiatric Neuroimaging Division 149 13th St, Charlestown, MA 02129 Phone: +1 617 643 7462 Email:heryil...@partners.org mailto:heryil...@partners.org ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh
You can just copy it over the old one (but make a backup of it first) On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote: Hi Doug, Thanks for your reply. I can certainly test it. Could you tell me how I can run this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' that I use is under '/usr/local/freesurfer/stable5_0_0/bin/' Best, Hamdi From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, September 08, 2014 11:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh That was an oversight. I've attached a version that should work. Can you test it for me? Once I know it works I'll check it in to tree. doug On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote: Dear FS experts, I have a question about a MC output file. When I run the MC sim (using mri_glmfit-sim) on the surface, it generates a bunch of files including a 'sig.masked.mgh', which is nice for displaying the significance map limited to the clusters that survive the MC correction. However, when I run it on the volume, it doesn't generate this specific file. Does anyone know the reason for that? Is there an alternative way to display the significance map that show only the clusters that survive the MC correction? Many thanks! Hamdi -- Hamdi Eryilmaz, PhD Massachusetts General Hospital A.A. Martinos Center for Biomedical Imaging Psychiatric Neuroimaging Division 149 13th St, Charlestown, MA 02129 Phone: +1 617 643 7462 Email:heryil...@partners.org mailto:heryil...@partners.org ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh
Hi Doug, I don't seem to have the permission to change the contents of that folder. So I can't really copy it over. Is it possible to run this locally? I'm working on a linux workstation at Martinos and when I ask the source, it gives me that folder: which mri_glmfit-sim /usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, September 09, 2014 5:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh You can just copy it over the old one (but make a backup of it first) On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote: Hi Doug, Thanks for your reply. I can certainly test it. Could you tell me how I can run this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' that I use is under '/usr/local/freesurfer/stable5_0_0/bin/' Best, Hamdi From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, September 08, 2014 11:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh That was an oversight. I've attached a version that should work. Can you test it for me? Once I know it works I'll check it in to tree. doug On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote: Dear FS experts, I have a question about a MC output file. When I run the MC sim (using mri_glmfit-sim) on the surface, it generates a bunch of files including a 'sig.masked.mgh', which is nice for displaying the significance map limited to the clusters that survive the MC correction. However, when I run it on the volume, it doesn't generate this specific file. Does anyone know the reason for that? Is there an alternative way to display the significance map that show only the clusters that survive the MC correction? Many thanks! Hamdi -- Hamdi Eryilmaz, PhD Massachusetts General Hospital A.A. Martinos Center for Biomedical Imaging Psychiatric Neuroimaging Division 149 13th St, Charlestown, MA 02129 Phone: +1 617 643 7462 Email:heryil...@partners.org mailto:heryil...@partners.org ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] New deadline for the Alzheimer's Disease Sage/DREAM Challenge!
We have extended the Alzheimer's Disease Sage/DREAM Challenge #1 submission period to October 17th -- Time to enter! https://www.synapse.org/#!Synapse:syn2290704 Of particular interest to the members of this mailing list is subchallenge 3, which leverages brain imaging ( FreeSurfer was used in the processing of the data ) , in addition to genetics, cognitive assessments, and demographic information from cohorts ranging from cognitively normal to mild cognitively impaired to individuals with AD. Looking forward to your submissions to the leaderboard!: https://www.synapse.org/#!Synapse:syn2290704/wiki/65302 Cheers, @rno ___ 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] Monte Carlo Sim output / sig.masked.mgh
Yes, you can just run /path/to/your/local/copy/mri_glmfit-sim On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote: Hi Doug, I don't seem to have the permission to change the contents of that folder. So I can't really copy it over. Is it possible to run this locally? I'm working on a linux workstation at Martinos and when I ask the source, it gives me that folder: which mri_glmfit-sim /usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, September 09, 2014 5:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh You can just copy it over the old one (but make a backup of it first) On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote: Hi Doug, Thanks for your reply. I can certainly test it. Could you tell me how I can run this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' that I use is under '/usr/local/freesurfer/stable5_0_0/bin/' Best, Hamdi From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, September 08, 2014 11:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh That was an oversight. I've attached a version that should work. Can you test it for me? Once I know it works I'll check it in to tree. doug On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote: Dear FS experts, I have a question about a MC output file. When I run the MC sim (using mri_glmfit-sim) on the surface, it generates a bunch of files including a 'sig.masked.mgh', which is nice for displaying the significance map limited to the clusters that survive the MC correction. However, when I run it on the volume, it doesn't generate this specific file. Does anyone know the reason for that? Is there an alternative way to display the significance map that show only the clusters that survive the MC correction? Many thanks! Hamdi -- Hamdi Eryilmaz, PhD Massachusetts General Hospital A.A. Martinos Center for Biomedical Imaging Psychiatric Neuroimaging Division 149 13th St, Charlestown, MA 02129 Phone: +1 617 643 7462 Email:heryil...@partners.org mailto:heryil...@partners.org ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_convert
How many files are in the dicom folder? Try copying one of them to a different folder and running it on that one file (it will only be a test, the output file will not be correct) On 9/9/14 1:12 PM, Nooshin Zadeh wrote: Yes. It just hang there. I even let it run for few days! and no outcome. On Sep 9, 2014 12:19 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Nooshin does it just hang there? How long do you let it run? Bruce On Tue, 9 Sep 2014, Nooshin Zadeh wrote: Dear FreeSurfer experts, I get a new message when I use mri_convert command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file, and goes to infinite loop. mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards, Nooshin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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.
