Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)

Oops, never mind. User error. I’m too embarrassed to even explain what I did. :) Joe > On Feb 29, 2016, at 21:38, Joseph Dien wrote: > > Hi, > I’m having an fsgd error that has totally stumped me. I’m trying to run > the following command to compute the second level

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Those numbers only refer to the color the too will appear: hence the name color lookup table hth d Sent from my Phone > On Mar 1, 2016, at 21:33, Faeze Vedaei wrote: > > Thank you for your response. It is better to explain my question that the > coordinates for

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Thank you for your response. It is better to explain my question that the coordinates for paracentral in .ctab file is '63 100 60', that you changed these to '23 230 60' in your new version. My question is that how you applied such this change on the RBG values for this region? Regards, Faezeh

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

It is just a text file (you can open it with vi or gedit whatever), just add new lines for new labels and make the colors the color you want them to be.\ hth d On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei wrote: > Thank you so much for you response. I should say that I

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Thank you so much for you response. I should say that I know about what you are saying. My issue is that I have these 4 columns in my LUT file. Why and how can I change the numbers (RGB values) to create new LUT? Bests, Faezeh On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei

Re: [Freesurfer] running two versions of fs in the same

is it just the BA labels you want out of the newer version? If so, just change your FREESURFER_HOME to point at the new version after your 5.1 recon-all is done and run the -dobalabels target with the dev recon-all cheers Bruce On Tue, 1 Mar 2016, Fengji Geng wrote: Hi Bruce,   The

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

The 4 number columns represent: Red Green Blue and Alpha The numbers range from 0-255. They can be combined to create any color. Play around, and you will see what it does. hth, d On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei wrote: > Hi, > > Thank you so much for you

Re: [Freesurfer] running two versions of fs in the same

Hi Bruce, The command that we ran is recon-all. Below is the error msg: mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label --trgsubject HMN122 --trglabel ./lh.BA2.label --hemi lh --regmethod surface No such file or directory

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi, Thank you so much for you descriptions. I checked out the link you just sent me. Because I do not have many experiences working with Freesurfer, I really could not understand about how I can do such this revising in LUT file. Can you explain more about this? I truly appreciate your time and

Re: [Freesurfer] mri_label2vol projfrac missing voxels

Hi, I just wanted to post back the problem was solved (Thanks Doug). The solution is this: 1. use mri_aparc2aseg mri_aparc2aseg --s $SUBJECT --o .mgz --annot --annot-table [Note, in my case I was using 3 different values, 1, 2, 3 for the labels with only left hemisphere labels (the details

Re: [Freesurfer] running two versions of fs in the same dataset

Hi Fengji you need to give us more details about the problems before we can help you. What commands failed? What was the screen output? Note that there is still no such thing as FS 6.0. We are hoping to have it in the relatively near term, but it doesn't exist yet. cheers Bruce On Tue, 1

Re: [Freesurfer] Entorhinal Cortex segmentation and volume

Hi Melina Sorry for the delay in responindg, can you tell us a bit more about the acquisition? They look very grainy and low contrast. Bruce On Mon, 16 Feb 2015, Melina Lehnerer wrote: > Thank you both for your respond. > 1. I have attached you some pictures. Like douglas wrote it

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Faezeh, Check this page out for details. The values are just numbers in the columns of the file: https://en.wikipedia.org/wiki/RGB_color_model hth d On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei wrote: > Hi, > > I really appreciate you for help me in this process. May

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi, I really appreciate you for help me in this process. May you clarify me from which pattern you changed the RGB values for that region? How I can change the coordinates for the others? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei wrote: > Hi,

Re: [Freesurfer] Very urgent matlab command line to transform vol to label.

Try using this instead: mri_binarize --i file_created_by_vol_2_surf.mgz --min threshold --o bin.file_created_by_vol_2_surf.mgz mri_cor2label --i bin.file_created_by_vol_2_surf.mgz --id 1 ---l yourlabel.label On 02/27/2016 06:28 AM, std...@virgilio.it wrote: > Hi list, > I have read on your mail

Re: [Freesurfer] Map label from lh to rh

It does not. You can run mris_left_right_register. You will need to use mris_apply_reg instead of mri_label2label. See below. run with --help to get docs ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg On 02/25/2016 04:28 PM, Makaretz, Sara Johanna wrote: > Hi, I

Re: [Freesurfer] Permission denied error with mri_surfcluster command

can you send your command line and terminal output? On 02/25/2016 01:52 PM, Jennifer Legault wrote: > Hi Douglas, > > Thank you for all your help. When I say "volume" I do mean the FS > thickness*area measure. I ran the mri_glmfit with --osgm and for the > FWHM received the value of .925737.

Re: [Freesurfer] Fwd: View several Annot files in Tksurfer

you cannot load more than one in tksurfer. You can load load more than one in freeview. As Bruce points out, you cannot visualize more than one at a time (unless you mean the outline?) On 02/25/2016 06:06 PM, Bruce Fischl wrote: > Hi Faezeh > > the annotations label every vertex. How would you

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

yes, just follow the pattern of the file. You will probably want to use different RGB values to get different colored labels. hth d On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei wrote: > Hi, > > I should let you know that, it works! It shows paracentral name in tksurfer. >

Re: [Freesurfer] -qcache of v5.0 data with newer versions

Yes doug On 02/23/2016 03:00 PM, Daniel Ferreira wrote: > Dear experts, > > Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been > recon-all -all with FS 5.0.0? > > Thanks > > Dani > > > > ___ > Freesurfer mailing list >

[Freesurfer] running two versions of fs in the same dataset

Dear fs developers, we are attempting to use the stable version of fs 5.1 for processing while also using the most current version for hippocampal segmentation on the same set of subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when the develop version of fs 6 was installed, we

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi, I should let you know that, it works! It shows paracentral name in tksurfer. So, how I have to revise my .ctab file to get the right result? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei wrote: > Hi, > > Thank you for your response. I just used

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

try now On 03/01/2016 02:16 PM, Versace, Amelia wrote: > > Hi, > > I am having the same issue. > > Can you please upload the updated version of epidewarp.fsl for FSL 5.x. > > Thanks a lot, Amelia > > *From:*freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu]

Re: [Freesurfer] Problem Installing FS

Odd. It should work so long as there is a "license.txt" file or ".license" file. Just for the sake of trying, what happens if you copy the "license.txt" file to ".license" so that you have both? $> cd /Applications/freesurfer $> cp license.txt .license And then try? -Zeke On 03/01/2016

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Faezeh, Please run the exact commands including the file I attached, not the aparc.annot.a2009s.ctab, and check the result using the freeview command I provided. Then let me know what label freeview shows. hth d On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei wrote: >

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

Hi, I am having the same issue. Can you please upload the updated version of epidewarp.fsl for FSL 5.x. Thanks a lot, Amelia From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Wednesday, February 10, 2016 10:58 PM To:

[Freesurfer] Problem Installing FS

Hi Zeke, I do have a file named license.txt in my FREESURFER_HOME directory as well as another one named LICENSE that comes with the FS installation. When I type: $> cd /Applications/freesurfer $> ls -l license.txt What happens is this: -rw-r--r--@ 1 carlosmillan staff 55 Feb 26 12:25

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi, Thank you for your response. I just used the command you suggested to use by just a change in calling .ctab LUT file. I used the path: 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just calling aparc.annot.a2009s.ctab. It is strange that I created annot file for

Re: [Freesurfer] Corrupted head surface with mkheadsurf?

It works but the magic number now is 2067208 and read_surf still does not read it On Mon, Feb 29, 2016 at 7:52 PM, Douglas N Greve wrote: > > try this version > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize > > > On 02/23/2016 10:17 AM,

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi Faezeh, It is strange that the LUT file you sent doesn't seem to be named anything similar to the file you called. You are calling new/002_S_0413/labels/aparc.annot.a2009s.ctab There also seem to be some basic issues with the command --s should just have the name of the subject not a

Re: [Freesurfer] Problem Installing Freesurfer

My guess is that pico did not actually save the license file because by default all directories under /Applications is protected. Which mean the "sudo" command is required. Do you definitely have a file called license.txt (or .license) in your FREESURFER_HOME directory? What happens when you

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

Hi, Here is the text format of those files. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei wrote: > Hi > > Thank you so much for your response. I attached here three files including > the command lines, LUT file , and the list of names I want to

Re: [Freesurfer] AAL atlas question

I'm actually wondering the same thing re AAL to subject space - this is what I have been using: spmregister - reg template to subject mri_label2vol - move AAL to subject space mri_segstats - pull in-volume stats using AAL in subject space mri_vol2surf - project AAL (subject space) to subject

[Freesurfer] Seeking postdoctoral candidates for datascience positions

We are seeking two postdoctoral computational/data scientists with a PhD in computer science, electrical or biomedical engineering, neuroscience, statistics, or related fields to apply for positions in the McGovern Institute for Brain Research at Massachusetts Institute of Technology. The

Re: [Freesurfer] Corrupted head surface with mkheadsurf?

I still get the error option --surf unkown On Mon, Feb 29, 2016 at 7:52 PM, Douglas N Greve wrote: > > try this version > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize > > > On 02/23/2016 10:17 AM, Maheen Siddiqui wrote: > > I changed the

Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

Hi Bruce, When I run the last stage of the ex-vivo processing (recon-all -cortribbon -sphere -surfreg -cortparc -parcstats -subjid $SUBID -noaseg), the parcellation labels come out in the wrong place. I haven't been able to figure out why this is happening, so I was wondering if its possible that

[Freesurfer] "wm" boundaries and stats

Freesurfer provides 34 ctx label volumes on each side of the brain with adjacent wm labels. The boundary between each ctx volume and the co-named adjacent wm volume is a third "white" label. I would like to extract a few pieces of information from the analogous boundary between each wm volume

Re: [Freesurfer] ineffective skull strip

Hi Lars sure, if you can a better strip give it a try. Dura is really hard to get rid of , and depending on your bandwidth and readout direction you also can find fat shifting down to touch the edge of cortex cheers Bruce On Tue, 1 Mar 2016, Lars M. Rimol wrote: Hi, We have run

Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

Hi John this is pretty puzzling. Is it causing any problems? tkmedit has been deprecated and it may just not be properly reading some header information or other. If nothing else is affected you can probably ignore it cheers Bruce On Mon, 29 Feb 2016, John Plass wrote: > Hi Bruce, > Thanks

[Freesurfer] Problem with brainstem substructures segmentation

Dear Freesurfer users, Sorry for reposting this message again, but I really need your help. We have downloaded the Freesurfer 6.0 version since we are really interested in the brainstem segmentation. We are working with a pc equipped with a 3.6 GHz CPU and 16 GB RAM. We installed freesurfer6.0