Re: [Freesurfer] autmatic image with panel of hemisphere made by script
Hi Thanks. Python was the first programing languages that I learned along with Java. Cheers Knut Jørgen On 08. feb. 2012 06:42, Michael Waskom wrote: Hi, On the off chance that you are comfortable with Python, you may find that PySurfer http://pysurfer.github.com/ provides a more pleasant scripting environment than the tcl-based TkSurfer interface :) Best, Michael On Tue, Feb 7, 2012 at 12:46 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Knut, you can check out my script called tksnap (uses accopanying mytks.tcl). It will take pics in different orientations. Note: this is not a supported script, so it's up to you to figure out what it does and how it does it. I provide it as a way to help you figure this stuff out. If you don't know csh and tcl, then it's not going to be much use to you. Good luck! doug ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tksnap ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mytks.tcl Knut J Bjuland wrote: Hi Bruce Is it possible to use ascript to create a similar figure to the jpg file I am attaching? Knut J On 07. feb. 2012 15:09, Bruce Fischl wrote: Hi Knut you can use a tcl script in tksurfer if you want. You are probably better off doing the 10^-log(p) on your own and saving it as a separate overlay. There are plenty of tcl scripts in the distribution as examples. A simple one would be: set val $home/$subject/label/$hemi.your_overlay.mgz puts loading overlay $val sclv_read_binary_values sclv_current_field redraw save_tiff $odir/$hemi.your_overlay.lateral.tif rotate_brain_y 180 redraw save_tiff $odir/$hemi.your_overlay.medial.tif put that in a file named something.tcl then load tksurfer with -tcl something.tcl I don't know about the 500dpi though, sorry. cheers Bruce On Tue, 7 Feb 2012, Knut J Bjuland wrote: I have used Tksurfer to make image from cross subject statistics maps in mgh files. Is it possible to use a script to make image with both hemisphere in lateral and medial view. I would also like to display p values as 10^-log(p). Is this possible? Can I use Matlat or FDR? How can I produce image with 500 dpi in tksurfer? Knut J ___ 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel: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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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] mris_divide_parcellation
Thank you Bruce, the parcellation looks good, as you say, I think that it doesn't affect me. yolanda 2012/2/7 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Yolanda does the resulting parcellation look ok? I think that's a small bug that may not have any effect on you (there will just be extra, unused color table entries) Bruce On Tue, 7 Feb 2012, Yolanda Vives wrote: Dear Freesurfer experts, I have a question regarding mris_divide_parcellation. I have created a file containing the parcels from aparc.annot that I want to split and I have run the following command. Why is Freesurfer allocating 36 additional units? When I open the new annotation file (rh.aparc.splitted) with matlab (using read_annotation), I can see that at the end of colortable.struct_names there are a lot of parcels called cluster38, cluster39, ..., cluster71. What are exactly these clusters? Many thanks, Yolanda In splittable.txt file precentral 2 Command ./mris_divide_parcellation fsaverage rh aparc.annot splittable.txt rh.aparc.splitted Output reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/amaebi_026/** users/buckner_cortical_atlas/**scripts/colortable_final.txt) interpreting 4th command line arg as split file name dividing precentral into 2 parts allocating new colortable with 36 additional units... saving annotation to rh.aparc.splitted writing colortable into annotation file... 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/**compliancelinehttp://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. -- Yolanda Vives PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Telf. +34 93 586 8232 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.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] Verifying ICV in FS5
Hi Jeff it looks pretty far off. Typically you want the surfaces to match the general shape of the brain cheers Bruce On Tue, 7 Feb 2012, Jeff Sadino wrote: Thank you Martin and Nick for the clarification about how to verify the talairach transformation in the newer FreeSurfers. I think I am going to use the -use-mritotal command, as this was giving more reasonable ICVs around 1.3L - 1.7L. I am still manually checking the outliers. According to the ICV measurement, this one seems way off, but I'm not sure how to judge the severity of the transform. On a scale of 1 to 10, 1 being bad, how would this one rate? How much would this cause the ICV to be off? Thank you, Jeff On Mon, Jan 30, 2012 at 8:47 AM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Jeff, to check the tal reg, use: tkregister2 --s subjid --fstal --surfs i've corrected the eTIV page to reflect this. --fstal loads mni305 as the target. the target used in the tal reg step (711-2C...) is registered with the mni305. note that --surfs is optional, as the surfaces may not exist yet. Nick On Fri, 2012-01-27 at 18:53 -0500, Martin Reuter wrote: Hi Jeff, I am not sure about which atlas, but concerning the transforms: 4.2 and earlier: talairach_with_skull.lta later versions: talairach.xfm I am pretty convinced that the way to check as described here http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV cd $SUBJECTS_DIR/subject/mri/transforms tkregister2 --xfm talairach.xfm \ --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca \ --mov ../nu_noneck.mgz --reg junk is correct in newer FS versions, but maybe double check with Nick. Best, Martin On Fri, 2012-01-27 at 13:39 -1000, Jeff Sadino wrote: bump :) any feedback on this would be very much appreciated. Thank you! Jeff On Mon, Jan 23, 2012 at 6:56 PM, Jeff Sadino jsadino.que...@gmail.com wrote: Hello, Thank you Nick, Martin, and Doug for your previous feedback about ICV. I have a couple more questions that I am hoping you could clarify for me. To verify my ICV value, some pages on the mailing list and wiki say to use this command: tkregister2 --s subject --fstal --surf Other places say to use this: tkregister2 --xfm talairach.xfm --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov ../nu_noneck.mgz --reg junk However, on this wiki page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV), it says that post fs4.2.0, the template is this file: 711-2C_as_mni_average_305.4dfp.img. In the first tkregister2 command above, doesn't the --fstal flag use the talairach template? But shouldn't it be using the 711 template? And since I am using fs5.0.0, does that mean that I should not be using the RB template? Ultimately, what is the correct way to verify the ICV in fs 5.0.0? Thank you very much, Jeff Sadino On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It's hard to tell from the coronal, but it looks ok. The problem is more visible in the sagittal. doug Jeff Sadino wrote: Hello Doug, I loaded up the tkregister2 program and I think I see some poor transformations. I've never really used it before though. Am I just looking at whether or not the green line lines up with the target image wm? Can you look at my pictures real quick? 040002_S04_test is from fs4 that is having problems. 040002_S04 is from fs3 and has a good icv value. Some of the blank spots are from my graphics drivers and unrelated to fs. tkregister2 also said the determinant of 040002_S04_test was 1.49544. Martin, Thank you for the idea. I did this, and got a much better icv. On fs3, where the icv was good, the number was 1,767,481. On fs4, it was 1,302,696. Using your idea on fs4, it was 1,819,485. Thank you so much to everyone for your help! Jeff On Thu, Feb 25, 2010 at 8:53 PM, Martin Kavec martin.ka...@gmail.com mailto:martin.ka...@gmail.com wrote: Hi Jeff, I see this relatively often. Eventhough the talairach registration is fine, the ICV is underestimated. In this case I take old ICV, which helps. mri_segstats --subject $MYSUBJECT --old-etiv-only This is in 99% of
Re: [Freesurfer] volume smoothing
Hi Holger you can try dilating and eroding the label (a morphological close) cheers Bruce On Wed, 8 Feb 2012, Klein, Holger wrote: Dear Freesurfers, Having used mri_label2vol I received a suitable volume that was slightly unsmooth unfortunately. I was looking for a proper command to ameliorate the smoothness of my volume but could not find a solution. Could anyone give me an advice to cope with that problem? Any help is greatly appreciated, Thanks in advance, Holger ___ 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] volume smoothing
Holger, you might also play with the fill threshold (--fillthresh) option. In the end, it can't be any smoother than your voxel size of course. doug Bruce Fischl wrote: Hi Holger you can try dilating and eroding the label (a morphological close) cheers Bruce On Wed, 8 Feb 2012, Klein, Holger wrote: Dear Freesurfers, Having used mri_label2vol I received a suitable volume that was slightly unsmooth unfortunately. I was looking for a proper command to ameliorate the smoothness of my volume but could not find a solution. Could anyone give me an advice to cope with that problem? Any help is greatly appreciated, Thanks in advance, Holger ___ 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.
[Freesurfer] Reposting: Question regarding DTI group analysis
Dear Experts, I completed my FA group analysis and I expect my FA to be larger in controls versus patients (based on the uncorrected results). I corrected by multiple comparisons using: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1000 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 so I have my: permcsd.sig.cluster.nii – map of significance of clusters permcsd.sig.ocn.nii and grf.th3.pos.sig.ocn.lut – segmentation of significant clusters permcsd.sig.cluster.summary – text file of cluster table (clusters, sizes, MNI305 XYZ, and their significances) 1) How can I visualize my results more exactly how I can visualize my uncorrected and corrected results. 2) How I can output in a table the FA values corresponding to each cluster? 3) If use tkmedit is the Functional value given me the FA values while moving the cursor or this Functional value represents something else in the case I plot: tkmedit cvs_avg35 norm.mgz \ -ov /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh \ -seg /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh \ /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut \ -fthresh 0.2 -fmax 1 Thank you very much, Antonella___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Reposting: Clusters by Multiple comparison
Hi Antonella, the right way to do it is to figure out what is going wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you send the log file? Should be permcsd.mri_glmfit-sim.log. If you need to run it for debugging purposes, you can run it with 10 iterations (change permcsd to permcsdtmp so you don't overwrite what is there). This should produce all the files, so if something is not there, it should be easy to track down why. doug Antonella Kis wrote: Dear Doug, When I run the: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters summary so as you recommended I am running the mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space? Thank you. AK -- 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 ?h.sulc and ?h.curv
They are computed from the ?h.white surface. The ?h.curv is the spatially smoothed mean curvature, and the ?h.curv is the integrated dot product of the movement vector with the surface normal during inflation. Therefore the curv is a local differential measure that will highlight small scale structure, while the sulc is insensitive to small local geometry and highlights larger scale structure (e.g. was the point deep even though it was folded out) On Tue, 7 Feb 2012, Jing Ming wrote: Hi surfers: I have a two questions. 1) how does freesurfer calculate ?h.sulc file and ?h.curv. Are they calculated after gray/white/csf segmentation? Are they calculate based on gray/white boundary? So, difference between ?h.sulc or ?h.curv will directly come from white matter change, right? 2) what's the difference between ?h.sulc and ?h.curv? In terms of sulcal structure, does ?h.sulc indicate sulcal depth and ?h.curv somehow indicate sulcal width? To me, from the display, ?h.sulc seems a smoothed version of ?h.curv. From some reference, I know .sulc is also called average convexity, so is the convexity for each vertex averaged within a small region or is it averaged through the whole hemisphere brain surface? Thanks much for your help! Best Jing ___ 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 ?h.sulc and ?h.curv
I think Bruce meant: the ?h.sulc is the integrated dot product of the movement vector with the surface normal during inflation. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, February 08, 2012 10:48 AM To: Jing Ming Cc: Freesurfer Subject: Re: [Freesurfer] Question about ?h.sulc and ?h.curv They are computed from the ?h.white surface. The ?h.curv is the spatially smoothed mean curvature, and the ?h.curv is the integrated dot product of the movement vector with the surface normal during inflation. Therefore the curv is a local differential measure that will highlight small scale structure, while the sulc is insensitive to small local geometry and highlights larger scale structure (e.g. was the point deep even though it was folded out) On Tue, 7 Feb 2012, Jing Ming wrote: Hi surfers: I have a two questions. 1) how does freesurfer calculate ?h.sulc file and ?h.curv. Are they calculated after gray/white/csf segmentation? Are they calculate based on gray/white boundary? So, difference between ?h.sulc or ?h.curv will directly come from white matter change, right? 2) what's the difference between ?h.sulc and ?h.curv? In terms of sulcal structure, does ?h.sulc indicate sulcal depth and ?h.curv somehow indicate sulcal width? To me, from the display, ?h.sulc seems a smoothed version of ?h.curv. From some reference, I know .sulc is also called average convexity, so is the convexity for each vertex averaged within a small region or is it averaged through the whole hemisphere brain surface? Thanks much for your help! Best Jing ___ 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 ?h.sulc and ?h.curv
oops, thanks Matt Bruce On Wed, 8 Feb 2012, Matt Glasser wrote: I think Bruce meant: the ?h.sulc is the integrated dot product of the movement vector with the surface normal during inflation. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, February 08, 2012 10:48 AM To: Jing Ming Cc: Freesurfer Subject: Re: [Freesurfer] Question about ?h.sulc and ?h.curv They are computed from the ?h.white surface. The ?h.curv is the spatially smoothed mean curvature, and the ?h.curv is the integrated dot product of the movement vector with the surface normal during inflation. Therefore the curv is a local differential measure that will highlight small scale structure, while the sulc is insensitive to small local geometry and highlights larger scale structure (e.g. was the point deep even though it was folded out) On Tue, 7 Feb 2012, Jing Ming wrote: Hi surfers: I have a two questions. 1) how does freesurfer calculate ?h.sulc file and ?h.curv. Are they calculated after gray/white/csf segmentation? Are they calculate based on gray/white boundary? So, difference between ?h.sulc or ?h.curv will directly come from white matter change, right? 2) what's the difference between ?h.sulc and ?h.curv? In terms of sulcal structure, does ?h.sulc indicate sulcal depth and ?h.curv somehow indicate sulcal width? To me, from the display, ?h.sulc seems a smoothed version of ?h.curv. From some reference, I know .sulc is also called average convexity, so is the convexity for each vertex averaged within a small region or is it averaged through the whole hemisphere brain surface? Thanks much for your help! Best Jing ___ 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] Longitudinal Processing, can I salvage cross-sectional edits during processing stream? Mark
Hi Mark, I talked to Allison and you should be able to rerun 5.1 on top of 5.0 but do NOT use the -clean flag (as it will delete your edits). Just make sure you make a backup copy of your data before doing this. Another thing: manual edits to the brainmask are treated differently from most manual edits in FreeSurfer and I am not sure exactly what will happen. I believe FreeSurfer keeps the brainmask.mgz if it is already there. This means that edits are kept, but also that your cross sectional analysis will still be biased, as tp1 brainmask was created with 5.0 (and will not be re-created) and tp2 brainmask was created with 5.1. You can recreate brainmask by simply deleting it (and brainfinalsurf and corresponding manedit files if exist) but then you will of course also loose your edits to those files. Now the good news. The way I implemented skull stripping in the longitudinal stream it uses a union of the cross sectional masks after registration in the base and also for the long runs (same mask for all of them). Thus, it removes the bias in the longitudinal processing. So you should be fine. Edits is a very complicated topic in the cross sectional processing for historic reasons, and also in longitudinal processing as it inherits some of those problems (but fixes some also :-). Best, Martin On Tue, 2012-02-07 at 22:46 -0500, Martin Reuter wrote: Hi Mark, So the first thing is you absolutely need to re-run you 1st year data with 5.1 The reason is that you will introduce potential bias by running the different time points with different software (consistently). As a side note: The same is basically true when they do software updates on the scanner which can void a study especially with only two time points. So the first thing is to figure out how to preserve your edits from 5.0 to 5.1 which should be possible (although I don't know how, maybe Allison or someone else knows)? Once that is done we will have to look into the edits in the long stream. It will probably depend on the types of edits you have. Some gets transferred automatically and some can be transferred. Best Martin On Feb 7, 2012, at 20:44, Mark Fletcher fletc...@illinois.edu wrote: Dear Everyone, First of all, I have been very impressed by the functionality and abilities of FreeSurfer. I have a question about the longitudinal processing stream. I have two sets of MRI at two different time points for elderly individuals. Before version 5.1 came out, I ran the first years data through the recon-all step while using version 5.0. Additionally, I made a substantial amount of corrections to many brain regions that I am hoping to not redo (with the number of subjects in my study it will take well over a month or two to re-do this). I collected my second years worth of data after 5.1 came out, and ran the recon-all on all of these subjects using version 5.1 of FreeSurfer. Similarly, I have already made corrections to this set of data as well. My ultimate goal is to now use the longitudinal processing stream. I think I understand the process, however, I am wondering if I need to re-do all of my corrections, or if I can salvage my corrections made from previous versions. I am a little concerned about what the -clean flag might do (will it eliminate my corrections?) Furthermore, while looking at your suggestions of editing errors, it says that you can save time because some changes only need to be made to the base. However, in my case, I think re-doing all of the edits will actually cost me much more time. I am willing to scrap all of my work if this is necessary, but I am wondering if there is a work-around. Sincerely, Mark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Reposting: Clusters by Multiple comparison
Hi Doug, Thank you very much for your help. I attached the log file. I can get the clusters summary if I run the mri_volcluster but it will give the correct clusters if I am not mentioning the --reg option? Also, when I am visualizing my clusters using tkmedit: tkmedit cvs_avg35 norm.mgz \ -ov /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh \ -seg /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh \ /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut \ -fthresh 0.2 -fmax 1 I can read the functional value for each cluster. What exactly this value represents? Is my FA value or -log10(p)? How can I get my FA values within each cluster in a table? Thank you so much. Antonella From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, February 8, 2012 11:37 AM Subject: Re: Reposting: Clusters by Multiple comparison Hi Antonella, the right way to do it is to figure out what is going wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you send the log file? Should be permcsd.mri_glmfit-sim.log. If you need to run it for debugging purposes, you can run it with 10 iterations (change permcsd to permcsdtmp so you don't overwrite what is there). This should produce all the files, so if something is not there, it should be easy to track down why. doug Antonella Kis wrote: Dear Doug, When I run the: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters summary so as you recommended I am running the mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space? Thank you. AK -- 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. permcsd.mri_glmfit-sim.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Reposting: Clusters by Multiple comparison
Oh, ok, I remember this now. Yes, you can use your mri_volcluster command below the clusters. To get the table, run mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i fa.nii.gz --avgtwf fa.avg.dat --sum permcsd.sig.cluster.summary The fa.avg.dat will have a table of data. Each row will be a subject, each column a cluster (matching that found in permcsd.sig.cluster.summary) doug Antonella Kis wrote: Hi Doug, Thank you very much for your help. I attached the log file. I can get the clusters summary if I run the mri_volcluster but it will give the correct clusters if I am not mentioning the --reg option? Also, when I am visualizing my clusters using tkmedit: tkmedit cvs_avg35 norm.mgz \ -ov /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh \ -seg /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh \ /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut \ -fthresh 0.2 -fmax 1 I can read the functional value for each cluster. What exactly this value represents? Is my FA value or -log10(p)? How can I get my FA values within each cluster in a table? Thank you so much. Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, February 8, 2012 11:37 AM *Subject:* Re: Reposting: Clusters by Multiple comparison Hi Antonella, the right way to do it is to figure out what is going wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you send the log file? Should be permcsd.mri_glmfit-sim.log. If you need to run it for debugging purposes, you can run it with 10 iterations (change permcsd to permcsdtmp so you don't overwrite what is there). This should produce all the files, so if something is not there, it should be easy to track down why. doug Antonella Kis wrote: Dear Doug, When I run the: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters summary so as you recommended I am running the mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space? Thank you. AK -- 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] Question about ?h.sulc and ?h.curv
Thanks, Bruce and Matt. bestJingDate: Wed, 8 Feb 2012 11:53:44 -0500 From: fis...@nmr.mgh.harvard.edu To: m...@ma-tea.com CC: freesurfer@nmr.mgh.harvard.edu; mj_com...@hotmail.com Subject: Re: [Freesurfer] Question about ?h.sulc and ?h.curv oops, thanks Matt Bruce On Wed, 8 Feb 2012, Matt Glasser wrote: I think Bruce meant: the ?h.sulc is the integrated dot product of the movement vector with the surface normal during inflation. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, February 08, 2012 10:48 AM To: Jing Ming Cc: Freesurfer Subject: Re: [Freesurfer] Question about ?h.sulc and ?h.curv They are computed from the ?h.white surface. The ?h.curv is the spatially smoothed mean curvature, and the ?h.curv is the integrated dot product of the movement vector with the surface normal during inflation. Therefore the curv is a local differential measure that will highlight small scale structure, while the sulc is insensitive to small local geometry and highlights larger scale structure (e.g. was the point deep even though it was folded out) On Tue, 7 Feb 2012, Jing Ming wrote: Hi surfers: I have a two questions. 1) how does freesurfer calculate ?h.sulc file and ?h.curv. Are they calculated after gray/white/csf segmentation? Are they calculate based on gray/white boundary? So, difference between ?h.sulc or ?h.curv will directly come from white matter change, right? 2) what's the difference between ?h.sulc and ?h.curv? In terms of sulcal structure, does ?h.sulc indicate sulcal depth and ?h.curv somehow indicate sulcal width? To me, from the display, ?h.sulc seems a smoothed version of ?h.curv. From some reference, I know .sulc is also called average convexity, so is the convexity for each vertex averaged within a small region or is it averaged through the whole hemisphere brain surface? Thanks much for your help! Best Jing ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Reposting: Clusters by Multiple comparison
What I have listed as fa.nii.gz should be the same file that you passed to mri_glmfit with the --y option. doug Antonella Kis wrote: Dear Doug, THANKS SO MUCH for your help. My last questions is: I suppose the --i fa.nii.gz is an input file. What should be my input in thi scase if for each subject I have different fa values and gor the mri_glmfit I used the GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz which is the concanetated masked file resampled to the CVS space. Should I use this file or what exactly for the fa.nii.gz? Also will mri_volcluster but it will give the correct clusters if I am not mentioning the --reg option? MAny thanks and have a great day! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, February 8, 2012 1:50 PM *Subject:* Re: Reposting: Clusters by Multiple comparison Oh, ok, I remember this now. Yes, you can use your mri_volcluster command below the clusters. To get the table, run mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i fa.nii.gz --avgtwf fa.avg.dat --sum permcsd.sig.cluster.summary The fa.avg.dat will have a table of data. Each row will be a subject, each column a cluster (matching that found in permcsd.sig.cluster.summary) doug Antonella Kis wrote: Hi Doug, Thank you very much for your help. I attached the log file. I can get the clusters summary if I run the mri_volcluster but it will give the correct clusters if I am not mentioning the --reg option? Also, when I am visualizing my clusters using tkmedit: tkmedit cvs_avg35 norm.mgz \ -ov /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh \ -seg /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh \ /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut \ -fthresh 0.2 -fmax 1 I can read the functional value for each cluster. What exactly this value represents? Is my FA value or -log10(p)? How can I get my FA values within each cluster in a table? Thank you so much. Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, February 8, 2012 11:37 AM *Subject:* Re: Reposting: Clusters by Multiple comparison Hi Antonella, the right way to do it is to figure out what is going wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you send the log file? Should be permcsd.mri_glmfit-sim.log. If you need to run it for debugging purposes, you can run it with 10 iterations (change permcsd to permcsdtmp so you don't overwrite what is there). This should produce all the files, so if something is not there, it should be easy to track down why. doug Antonella Kis wrote: Dear Doug, When I run the: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters summary so as you recommended I am running the mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space? Thank you. AK -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto: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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:
[Freesurfer] Defects in freesurfer output
Hello, I am getting defects in the volume output of freesurfer with respect to the pial surface and whilte-matter surface boundary. I am wanting to measure the cortical thickness after running recon_all. I was inspecting the pial and white surface using tkmedit and I noticed (volume data view using tkmedit) that in most of my subjects the freesurfer has included non-cortical matter (ex: cerebellar regions) as cortical matter and have excluded several white matter voxels. I use brainmask volume loaded as main volume and white matter volume loaded as aux volume to inspect the final pial and white surfaces. These defects are more clearly visible when I get the subcortical segmentation in on mode to be viewed or when I am viewing the pial/white surface boundaries in the images where brainmask is loaded as main volume with T1.mgz as the aux volume and subcortical segmantation in on mode. Interestingly such defects were found in same regions across the subject and are present in more than one section. If what I am seeing are defects, this would be require too much editing. I am very new to freeSurfer, please advise. Rashmi. This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. ___ 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_compile_edits
Mike, Hi, what you describe is a bug in mri_compile_edits. I've posted a fixed version for linux here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4/mri_compile_edits N. On Thu, 2012-02-02 at 14:51 -0600, Michael Harms wrote: Hi Nick, Why does mri_compile_edits (-showedits flag) report edits to brainmask.mgz (both in the edits.mgz volume and its text output) if no manual edits were actually performed -- i.e, if brainmask.mgz and brainmask.auto.mgz are identical? thanks, -MH ___ 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 Lab seeks Research Assistant
Please forward to anyone you think may be interested: Position involves working in a fast-paced Computational Neuroimaging Lab. The lab develops and maintains software for MR image analysis and works primarily in a UNIX environment. The lab is also responsible for several in vivo and ex vivo (human) MRI projects. We are seeking a Research Assistant to take on several job responsibilities from a list of potential responsibilities. The Research Assistant would be responsible for work on several projects. One major project would be assisting with the scanning for the Vietnam Era Twin Study of Aging (VETSA), a large-scale research project on cognitive aging in twins. Scans are early Wednesday and Saturday mornings, every week, March through August and every other week (or less) for the rest of the year. In addition to the above, the Research Assistant would help with high resolution ex vivo scanning projects on the 3 and 7 Tesla MRI scanners. Candidate must be willing to work evenings and weekends to perform some of the experiments, including being on call during designated weekends to respond to technical problems. Candidate must also be comfortable interacting with brain tissue. Other potential projects may include: -Quality checking in vivo MRI data that has been processed by the FreeSurfer software package and manually fixing errors. -Debugging and testing specific elements of FreeSurfer. For this and the above project, the candidate must be comfortable with computers and beta testing software. -Assisting with histological processing: sectioning, mounting, histochemical and immunocytochemical staining. -Manually labeling in vivo and ex vivo MRI images. Candidate should be able to work independently, show initiative, be confident in making decisions, able to multitask, not easily stressed, and one who is not easily discouraged by failed experiments but enjoys a challenge. Candidate should have a Bachelor's or Master's Degree. Relevant backgrounds would be Neuroscience, Psychology, Engineering, Computer Science, and/or Biology. A responsible individual with a flexible schedule is required. Experience in imaging and knowledge of UNIX and scripting is preferred. Knowledge of neuroanatomy or programming is a plus. Position offers great opportunities to work with prominent scientists, people from a variety of fields, a famous Research Center, a great and fun team, opportunities to publish, as well as guidance and support for future career choices. Please send resumes and cover letters to Allison Stevens at this email address. ___ 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] setting a cluster size and thresholding in tksurfer
Hi I am displaying the fMRI results in tksurfer. Is there a way in tksurfer to set a cluster size (for eg 50 vertices) and display only those activated regions which have bigger clusters than 50 ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Error - Need help
Is there any way that after this change , the execution will start exactly where it failed . Or do I need to start all over again Regards - Original Message - Darshan, copy the fsaverage subject from $FREESURFER_HOME/subjects to your $SUBJECTS_DIR n. 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
