[Freesurfer] A question about VirtualBox version of FreeSurfer Ver 5.0

Hi, there, I tried to use the VirtualBox version of FreeSurfer Ver 5.0 (I downloaded freesurfer-Virtualbox-linux-x86-stable-pub-v5.0.0-full.vdi) My system is Windows 7 64-bits, the VirtualBox I am using is Version 3.2.10 r66523, I tried to select Ubuntu and Ubuntu 64-bits as the guest OS

Re: [Freesurfer] longitudinal base error

again. Best Martin On 28.10.2010, at 20:24, Guang Zeng wrote: Hi, there, %% After running this command with FS v4.5 : recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force %% I get the following error: mri_concatenate_lta -in

[Freesurfer] What is FreeSurfer V5.0 doing after -wmparc in -autorecon3

Hi, there, In FS Ver4.5.0, -wmparc is the last step of -autorecon3. Recently, I tested FS Ver5.0, it looks like -wmparc is not the last step of -autorecon3 now, right? I noticed that it still ran several steps after -wmparc, Anyone can give a brief introduction about the -autorecon3 step of FS

Re: [Freesurfer] longitudinal base error

lease notes) and run again. Best Martin On 28.10.2010, at 20:24, Guang Zeng wrote: Hi, there, %% After running this command with FS v4.5 : recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force %% I get the following

[Freesurfer] longitudinal base error

Hi, there, %% After running this command with FS v4.5 : recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force %% I get the following error: mri_concatenate_lta -invert1 005_S_0221_45_20070321.105506_1_to_005_S_0221BASE.lta identity

[Freesurfer] freesurfer 5.0 in ubuntu 10.04

Hi, there, I just downloaded and installed freesurfer 5.0 under Ubunto 10. The version I am downlaoded is freesurfer-Linux-centos4-stable-pub-v5.0.0.tar.gz I ran a subject, but it failed at the first step, the error message I got is: talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm

Re: [Freesurfer] how to expand the disk size if I use VirtualBoxFS45

size if I use VirtualBoxFS45 > > You can create another virtual disk and attach to your virtual machine > > -- via iPhone iOS4 > > Em 22/08/2010, às 16:16, Guang Zeng escreveu: > > > Hi, there, > > > > I am using VirtualBoxFS45 now, everything is fine

Re: [Freesurfer] how to expand the disk size if I use VirtualBoxFS45

45 > > You can create another virtual disk and attach to your virtual machine > > -- via iPhone iOS4 > > Em 22/08/2010, às 16:16, Guang Zeng escreveu: > > > Hi, there, > > > > I am using VirtualBoxFS45 now, everything is fine. > > But I find that after

[Freesurfer] how to expand the disk size if I use VirtualBoxFS45

Hi, there, I am using VirtualBoxFS45 now, everything is fine. But I find that after I load the FSVirtualBox.vdi, the default storage space is about 8GB. I'd like to use FreeSurfer to run multiple subjects (about 100), and then do group analysis using QDEC, however the 8GB disk space limit wil

Re: [Freesurfer] a question about VirtualBoxFS4.5

those files or directory. You should probably ask a sysadmin to do it or if you have admin access, you can probably do something like sudo The sudo command will prompt you type the root password. --Thomas On Aug 22, 2010, at 11:25 AM, Guang Zeng wrote:Hi, there, I am using VirtualBox45 now

[Freesurfer] a question about VirtualBoxFS4.5

Hi, there, I am using VirtualBox45 now. After I installed it, I tested it using tkmedit and tksurfer command, everything looks ok. However, when I try to run a recon-all command, it fails at the mris_volmask step, the error mask I got is: "mris_volmask.bin: error while loading shared librari

[Freesurfer] how to set the tkmedit window size

Hi, there, When I load a subject volume via Tkmedit, is it possible that we can set the Tkmedit main window to a fixed size by tkmedit commandlines? I am kind of tired of dragging the window and resizing it after viewing 100 subejcts. Thanks a lot! Guang

[Freesurfer] how to svae FreeSurfer space?

Hi, there, I have used FreeSurfer cross-sectional and longitudinal stream to process more than 1000 subjects, and the output file occupied almost all my storage space. Currently, I am thinking about delete some FreeSurfer output files to save some storage space, What I am think now is: 1.

[Freesurfer] transversetemporal data is missing in rh.aparc.stats

Hi, there, I have a subject which is processed through FreeSurfer longitudinal stream, and I found that in the rh.aparc.stats file, the data of transversetemporal is not included. So, when FreeSurfer can not detect a ROI, it will not write it into ?h.aparc.stats ? Thanks! Guang

[Freesurfer] how the -nonuintensitycor flag work?

Hi, there, I wan to use the -nonuintensitycor option of the recon-all command, my command line is: recon-all -s subjid -all -nonuintensitycor, But the process failed because in the following step, they can not find nu.mgz, so I need to create my own nu.mgz before running my recon-all command,

Re: [Freesurfer] how to QC hippocampal measurement

: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] how to QC hippocampal measurement > > Hi Guang, > > there are some tools in slicer for making flythrough movies you could use > to make a quick check. > > cheers, > Bruce > > On Thu, 4 Feb 2010, Guang Zeng

Re: [Freesurfer] negative ICV volume

: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] negative ICV volume > > Hi Guang, > > check your talairach transform to see if it failed. > > cheers > Bruce > On Fri, 14 May 2010, > Guang Zeng wrote: > > > > > Hi, there, > > > > R

[Freesurfer] negative ICV volume

Hi, there, Recently, I ran a subject through FreeSurfer 4.5.0. I load the segmentation results using tkmedit, it looks fine to me. But, from both aseg.stats and wmparc.stats, I read a negative ICV volume, # subjectname 01290403_20080924 # BrainMaskFile mri/brainmask.mgz # BrainMaskFileTimeS

[Freesurfer] a 3T MPRAGE subject fails at mri_ca_label

Hi, there I have a 3T MPRAGE subject which fails at the mri_ca_label step, the recon-all.log is pasted below, Any suggestions to fix this error? Thanks a lot! Guang mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/biotools/freesurfer/freesurfer-v4.5.0/average/

[Freesurfer] a question about mri_robust_template

Hi, there, I have a question about mri_robust_template, I have a binary brainmask for each time point, I'd like to create a binary norm_template.mgz using mri_robust_template command. Has mri_robust_template an option to do nearest interpolation ? Thanks! Guang

Re: [Freesurfer] Is this longitudinal result correct

: [Freesurfer] Is this longitudinal result correct Hi Guang, what do you mean with 'longitudinal brainmask'?You need to overlay the segmentation to the brainmask in the longitudinal subject dir. The brainmask in the base dir is in a different space. Best Martin On Apr 6, 2010, at 11:29,

Re: [Freesurfer] FW: how to modify the wm.mgz

You could copy the SPM > results to wm.mgz and proceed from there I think, or you can use the expert > options to correct the intensity thresholds > > cheers, > Bruce > > > On Tue, 30 Mar 2010, Guang Zeng wrote: > > > > > Hello, Bruce, > > > > Thank

[Freesurfer] calculate the average thickness of a ROI around PCC

Hi, there, I'd like to measure the average thickness of a ROI around PCC (posterior cingulate cortex). I only have its MNI152 coordinate (-2, -45, 34). How can I calculate its corresponding RAS and Talaraich coordinate, is there an equation? Thanks! Guang

Re: [Freesurfer] the thickness of manually selected vertex

1-based indices in matlab? Also, please post > these to the list so that others can answer! > On Thu, 25 Mar 2010, Guang Zeng > wrote: > > > > > Using mris_anatomical_stats, I got > > > > table columns are: > >number of vertices > >total surface

Re: [Freesurfer] the thickness of manually selected vertex

ess of manually selected vertex > > Q1: yes. > Q2: do you want each of them individually or the average? You can save a > label file of the 4 vertices and use mris_anatomical_stats to get the > average > > cheers > Bruce > > On Wed, 24 Mar 2010, Guang Zeng wr

Re: [Freesurfer] the thickness of manually selected vertex

gt; Subject: Re: [Freesurfer] the thickness of manually selected vertex > > Q1: yes. > Q2: do you want each of them individually or the average? You can save a > label file of the 4 vertices and use mris_anatomical_stats to get the > average > > cheers > Bruce > > On Wed,

[Freesurfer] the thickness of manually selected vertex

Hi, there, I have two questions about the ?h.thickness file. If I load a subject's surface ?h.inflated using tksurfer, then I load its thickness file ?h.thickness, By clicking mouse on the surface, I can read the corresponding curvature value of a specific vertex. Q1, Here, the value next to

[Freesurfer] a question about wmparc.stats and aseg.stats

Hi, there, I have a question about wmparc.stats and aseg.stats, In aseg.stats, I read, # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1132816.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1156812, unitless # M

Re: [Freesurfer] recon-all fails because of mri_label error

...@hotmail.com Date: Sat, 13 Mar 2010 17:03:05 -0500 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all fails because of mri_label error What version are you running? On Mar 13, 2010, at 4:22 PM, Guang Zeng wrote: Hi, there, recon-all fails because of mri_label error , I copied the

Re: [Freesurfer] recon-all fails because of mri_label error

rror What version are you running? On Mar 13, 2010, at 4:22 PM, Guang Zeng wrote: Hi, there, recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions? gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0

[Freesurfer] recon-all fails because of mri_label error

Hi, there, recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions? gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.1

Re: [Freesurfer] modification made to longitudinal results

h). If there is demand, I will put > priority on this and make it available. > > Best, Martin > > On Thu, 2010-02-25 at 09:16 -0600, Guang Zeng wrote: > > Hi, there, > > > > I need add some control points to the longitudinal results. > > After adding control

[Freesurfer] freesurfer atlas and template

Hello, there, I have two questions about FreeSurfer default atlas and template, Will Freesurfer team build an atlas or template using 3T scans in future? Will Freesurfer team build an atlas or template using patients with disease in future? Thanks! Guang

[Freesurfer] a question about FS longitudinal stream

Hi, there, I have a question about FS longitudinal stream, I have data from two time points which have been processed by FreeSurfer cross-sectional stream. I also built the base template using recon-all -base command, everything looks fine. When I ran the longitudinal stream, one of them stop

[Freesurfer] how to use time points

Hi, there, I have scans from two time points, and they have been cross-sectionally processed. But both of they missed some white matter in some slices, so I manually add control points to them, and re-run it. Both of them look fine now. Then, I send them to longitudinal stream. After the -ba

[Freesurfer] modification made to longitudinal results

Hi, there, I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should I use? recon-all -s subj.long.baseid or recon-all -long subj baseid Thanks! Guang ___

[Freesurfer] convert vertex in tksurfer to point in tkmedit

Hello, there, I load lh.inflated of a subject using tksurfer, click a point (or vetex), then Click "Save Point") Meanwhile, I load the same subject in tkmedit, select "goto save point", I can see the saved point. If I try to convert multiple points (or vertices) from tksurfer to tkmedit, is t

[Freesurfer] cross-sectional analyis error

Hi, there, I am testing two subjects using cross-sectional FS. Both of they have being processed for almost four days. Both of them are stuck at the mris_fix_topology step, but there is no error message pops up. Subject#1 * INFO: ass

[Freesurfer] a question about rebuild_gca_atlas.csh

Hi, there, I am using the rebuild_gca_atlas.csh to build our own subcortical atals now, and met a problem at the second step which is # Train using ONE_SUBJECT, the command line is: mri_ca_train -prior_spacing 2 -node_spacing 8 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_man.xf

[Freesurfer] tksurfer fill holes

Hi, there, Is there are a command-line version of that 'Fill holes", "Dilate" and "Erode" options in tksurfer. Could I select the size of the kernel for dilation and erosion? Thanks! Guang ___

[Freesurfer] diagnostic level

Hi, there, Both mris_ca_label and mris_ca_train have a -v option which is called: diagnostic level. What is the meaning of this diagnostic level? Thanks! Guang _ Hotmail: Trusted email wit

[Freesurfer] how to QC hippocampal measurement

Hi, there, I have used FreeSurfer to measure the hippocampal size of 200 ADNI subjects, and now I'd like to QC the hippocampal measurement. Anyone can give me some suggestion to do this, instead of loading they one-by-one ? Thanks! Guang _

Re: [Freesurfer] a question about mris_ca_train

egmentation directly to an annotation, then use > mri_annotation2label to convert the annotation into a set of labels. > Nothing here guarantees that labels will be connected or contiguous nor > is it sure that all vertices on the surface will be labeled. > > doug > > Guang

[Freesurfer] where can I find write_annotation.m

Hello, there, Where can I download write_annotation.m, I can not find it in my /matlab folder. Thanks! Guang _ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/

[Freesurfer] FreeSurferColorLUT label Unkown in annotation file

Hi, there, I have question about FreeSurferColorLUT label Unkown in annotation file. In FreeSurferColorLUT, I read that #No. Label Name:R G B A 0 Unknown 0 00 0 I load the inflated surface of a subject, import

[Freesurfer] why FreeSurfer Surface Atlas does not contain subcortical region

Hi, there, Kind of wondering, why FreeSurfer Surface Atlas does not contain subcortical region? Thanks! Guang _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go

[Freesurfer] rebuild_gca_atlas.csh question

Hi, there, I am running rebuild_gca_atlas.csh now, and met a problem at the first mri_ca_normalize step, my rebuild_gca_atlas.log file looks like below, \n\n mri_ca_normalize -mask /home/m047599/freesurfer-install/freesurfer/subjects_1.5T/STAND400_T1/mri/brain.mgz -seg /

[Freesurfer] Is there a bash version of rebuild_gca_atlas.csh

Hello, there, Is there a bash version of rebuild_gca_atlas.csh? Thanks! Guang _ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/196390710/direct/01/___

Re: [Freesurfer] how to view .gca file

labels.mgz > mri_convert atlas.gca#2 priors.mgz > > cheers, > Bruce > > p.s. sorry, I don't think the gca format is documented anywhere, but you > are welcome to the code if you want > > On Thu, 28 Jan 2010, Guang Zeng wrote: > > > > > Hello, Bruc

Re: [Freesurfer] how to view .gca file

ri_convert atlas.gca#1 priors.mgz labels.mgz > > to look at the most likely label and it's mean > > cheers, > Bruce > > On Thu, 29 Oct 2009, Guang Zeng > wrote: > > > > > Hi, there, > > > > I want to know how the FS GCA atlas looks like,

[Freesurfer] a question abourt FS longitudinal stream

Hi, there, I have a question about FS longitudinal stream, Suppose I have two volumes A and B, B is the copy of A, but has been scaled (say, 1%) at each direction. Both of them have been cross-sectionally processed. If we send them to the FS longitudinal stream, what will happen? For example,

[Freesurfer] FW: images with poor resolution

> -base triggers creation of the base subject, and requires the usual > additional flags to run the entire stream. -all is the what is > recommended here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing > > but you could also run the stages separately. >

Re: [Freesurfer] images with poor resolution

:47 -0500 > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] images with poor resolution > > also the base step > > On Mon, 2010-01-25 at 10:41 -0600, Guang Zeng wrote: > > Hello, Nick, > > > > I am using the latest 4.5.0. > > So I only

Re: [Freesurfer] images with poor resolution

n, 25 Jan 2010 12:34:47 -0500 > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] images with poor resolution > > also the base step > > On Mon, 2010-01-25 at 10:41 -0600, Guang Zeng wrote: > > Hello, Nick, > > > > I am using the latest 4.5.0.

Re: [Freesurfer] images with poor resolution

add those yourself to the > longitudinal stream. > > On Sat, 2010-01-23 at 22:02 -0600, Guang Zeng wrote: > > Hello, Nick, > > > > I read your answer to this thread posted few months ago. > > Currently, I met the same kind of problem, and I used the method

[Freesurfer] a question about control points

Hi, there, I have some scans which have poor white matter and gray matter contrast, and the results of the intensity normalization step are pretty bad. So I add some controls, the results looks much better now. But I met a question now, I sent these results-improved subjects to FS longitudina

Re: [Freesurfer] images with poor resolution

Hello, Nick, I read your answer to this thread posted few months ago. Currently, I met the same kind of problem, and I used the method you recommended below, it works pretty well on my cases. My question is: The results of my data have been improved in FS cross-sectional stream, if I want to

[Freesurfer] license problem

Hi, there, I installed FreeSurfer under my local directory few months ago. Last week, I copied all the FreeSurfer folder under my local directory (include .license file) to the /home directory of our group, so everyone can use it. However, it turns out that they can not use it even they can s

[Freesurfer] FreeSurfer two atalses

Hi, there, Are there any place in FreeSurfer Wiki or journal paper explain why FreeSurfer need to atlases; Subcortical and Surface? Thanks! Guang _ Hotmail: Trusted email with Microsoft’s

[Freesurfer] a question about rebuild_gca_atlas.csh

Hi, there, In rebuild_gca_atlas.csh, I read something like: # A talairach registration should be generated for this first subject as well, # in order to align the final atlas to the Talairach space. Is this talairach registration file the same as the talairach.xfm under each subject's /mri/tr

[Freesurfer] manually labeled subjects used for building the desikan_killiany gcs file

Hello, there, If it possible that I can view or download the manually labeled subjects you used for building the desikan_killiany gcs file from somewhere in the wiki? Thanks! Guang _ Hot

[Freesurfer] question about mris_ca_train

Hi, there, I have created our own template and am creating our own atlas now. I have annotation files for each subject in my training set, and my mris_ca_train command line is: mris_ca_train -n 2 -t /home/freesurfer-install/freesurfer/ATLASColorLUT.txt lh sphere.reg myatalas.annot cust

Re: [Freesurfer] a question about mris_ca_train

> see in tkmedit why the surface does not pass through your label. > > doug > > Guang Zeng wrote: > > Hello, Doug, > > > > Thanks a lot for your suggestion, I added --projfrac 0.5 to my > > vol2surf command, > > the result looks much better now, but the

[Freesurfer] a question about mris_ca_train

Hi, there, Recently, I sent sseveral emails to you to ask same kind of question about building our own template and atlas. Thanks a lot for your quick reply, they helps me a lot. Currently, I still have a question about building our own atlas using mris_ca_train, sorry to bother you again. W

Re: [Freesurfer] qdec output

: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] qdec output > > Try running mri_glmfit with the --help option. QDEC runs mri_glmfit. > > doug > > Guang Zeng wrote: > > Hi, there, > > > > Does anyone can give me link or paper which explains all

[Freesurfer] qdec output

Hi, there, Does anyone can give me link or paper which explains all the QDEC output file, such as F.mgh, gamma.mgh, beta.mgh ... What are they, how are they related? Thanks a lot! Guang __

[Freesurfer] how to evaluate our own template without creating our own atlas

Hi, there, We created our own template using 10 subjects, now we'd like to know how good it is compare to FS's default template. We do not create our own atlas yet which need manully label all the regions in the training set. Is there a way to do this kind of comparison? Is it possible to do

[Freesurfer] how to load lh.jacobian_white in tkmedit

Hi, there, I'd like to load lh.jacobian_white using tkmedit to check how much the white surface was distorted in order to register to the spherical atlas my command line is tkmedit subj_id brainmask.mgz rh.white -aux T1.mgz -aux-surface lh.jacobian_white -segmentation aseg.mgz $FREESURFER_HO

[Freesurfer] mris_volmask ERROR

Hi, there, I submit several subjects to FS piepline using our Sun Grid Engine System, all of them failed at the same place which is the mris_volmask step in autorecon3. It gave me an error like: ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 372 vtkMultiThreade

[Freesurfer] a question about the mris_volmask ERROR

Hi, there, I have question about the mris_volmask ERROR. I ran multiple subjects on our SUN Grid Engine system. sometimes some subjects are sent to the same cluster node, and limited memory is assigned to each subject. Because of this, I often met an ERROR at the mris_volmask --label_left_w

Re: [Freesurfer] how to convert our own atlas to freesurfer

to convert our own atlas to freesurfer > > oh, then you would just replace the .gca file in mri_em_register, > mri_ca_register, mri_ca_label and mri_ca_normalize > > cheers > Bruce > > On Thu, 3 Dec 2009, Guang > Zeng wrote: > > > > > Hello, Bruce,

Re: [Freesurfer] how to convert our own atlas to freesurfer

t our own atlas to freesurfer > > what kind of atlas? > On Wed, 2 Dec 2009, Guang Zeng wrote: > > > > > Hello, there, > > > > We have a manualled labeled atlas, it is saved in a .nii file. > > We'd liek to use this atlas instead of FS's default a

[Freesurfer] how to convert our own atlas to freesurfer

Hello, there, We have a manualled labeled atlas, it is saved in a .nii file. We'd liek to use this atlas instead of FS's default atlas. If there are any commands or fucntions in FS can help us to do it. Thanks a lot! Guang ___

[Freesurfer] (no subject)

Hi, there, I have made our own template using 20 subjects follwoing the instruction in FreeSurfer WIKI. (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates). I have a quesition now, Does the quality of the new template depends on the first subject I picked to built the tempalte

[Freesurfer] recon-all -qcache question

Hi, there, I have 60 subjects which have been FS analyzed without the flag -qcache. Now, I wan to do group analysis using QDEC. I need run recon-all -s subjectid -qcache for each of my subjects. Just want to know how it will take to finish the recon-all -s subjectid -qcache command for one s

[Freesurfer] a question about the output template by make_average_subject

hi, there, I called FS command make_average_subject to create an average subjects using 10 subjects. After the process finished, I found that there are two output template file, "lh.reg.template.tif" and "rh.reg.template.tif". How are these two templates different from the template I built by

[Freesurfer] how to use my own template

Hello, there, I built our own template, and gonna use it to test some subjects. Currently, I have two questions, (1) How can I use my template, In "recon-all.sh", I found that their two places where ?h.average.curvature.filled.buckner40.tif are called, so I just need to change all the "?h.a

[Freesurfer] repost a mris_make_template question

Hi, there, I am creating our own template now, and stucked at "Round 1" now (based on FreeSurfer WIKI description http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates). I found a thread posted a year ago and asked the same kind of question, (http://www.mail-archive.com/freesurfer@nm

Re: [Freesurfer] mris_make_template question

.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_make_template question > > no, you shouldn't run 2 and 3. sulc and curv are *not* surface formats, > so the code dies trying to read them as such > On Fri, 13 Nov 2009, Guang Zeng > wrote: > >

Re: [Freesurfer] mris_make_template question

m. > > cheers, > Bruce > On Thu, 12 Nov 2009, Guang Zeng wrote: > > > > > Hi, there, > > > > I am going to make our own template. Based on the introduction in > > FreeSurfer WIKI "The Surface Registration Process; Template", the first

[Freesurfer] mris_make_template question

Hi, there, I am going to make our own template. Based on the introduction in FreeSurfer WIKI "The Surface Registration Process; Template", the first step is "Prep". "The process starts ("Prep") by choosing one reference subject, and producing a template (Here, mytemp0.tif). No ?h.sphere is req

[Freesurfer] creat own template

Hi, there, I have two questions, 1. I have read "The surface registration and templates" at FreeSurfer WIKI, and I am going to creat our own registration template. Is there a shell script available somewhere to do this? 2. What are the files in the folder of ../freesurfer/subjects/fsaverag

[Freesurfer] (no subject)

Hi, there, I want to know how the FS GCA atlas looks like, is there a way to load the FS GCA Atlas and view it using tkmedit or matlab? Is it possible to replace FS Atlas with our own Atlas and use it for analysis? Thanks a lot! Guang

Re: [Freesurfer] TIV corrected

Freesurfer] TIV corrected > > no. > > douig > > Guang Zeng wrote: > > Hi, there, > > > > Have those volume of ROIs in aseg.stats been TIV corrected? > > > > > > > > > > Thanks a lot! > > > > Guang > > > > ---

[Freesurfer] TIV corrected

Hi, there, Have those volume of ROIs in aseg.stats been TIV corrected? Thanks a lot! Guang _ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/171222984/direct/

[Freesurfer] a question about mri_label_volume -eTIV

Hi, there, >From FS Wiki, eTIV - estimated Total Intracranial Volume, aka ICV, I read mri_label_volume requires specifying the transform file to use, and the scale factor: mri_label_volume -eTIV \ $sdir/transforms/talairach.xfm 1948 \ $sdir/aseg.mgz 17 53where $sdir is the path to the sub

[Freesurfer] volume difference in aparc.stats and wmparc.stats

Hi, there, I am looking at the volume size of front pole . In lh.aparc.stats, this volume is 590, while in wmparc.stats (it is called ctx-lh-frontalpole), this value is 610, which one is accurate? Thanks a lot! BTW: In FreeSurfer Tutorial : Process Flow (http://surfer.nmr.mgh.harvard.edu/fs

[Freesurfer] ?h.aparc.a2005s.stats and ?h.aparc.a2009s.stats

Hi, there, What is the difference between ?h.aparc.a2005s.stats (from ver 4.4) and ?h.aparc.a2009s.stats (from ver 4.5) in the stats folder? ?h.aparc.a2009s.stats is still based on Christophe's atlas, right? Thanks a lot! Guang ___

[Freesurfer] hippocampus volume difference

Hi, there, I use the following matlab code to find right and left hippocampus in aseg.mgz %% filename = 'case_1/mri/aseg.mgz'; [vol, M, mr_parms, volsz] = load_mgh(filename); hippo_left = find( (vol > 16.99) & (vol < 17.01) ); hippo_right = find( (vol > 52.99)

[Freesurfer] how to use mri_surf2surf

Hi, there, mri_surf2surf resamples one CorticalSurface onto another. If I have two subjects from different time points (tp1 and tp2), I'd like to compare the FreeSurfer analyzed surface data. For example, could I use mri_surf2surf to resample the white matter surface of tp1 onto tp2, so I c

Re: [Freesurfer] how to use mri_compute_seg_overlap

our second time point aseg is registered to the first. > if it is not, the your dices will be low, because its just comparing > voxel to voxel. > > Nick > > > On Wed, 2009-09-23 at 11:30 -0500, Guang Zeng wrote: > > Hi, there, > > > > I have two subjects

Re: [Freesurfer] how to use mri_compute_seg_overlap

s will be low, because its just comparing > voxel to voxel. > > Nick > > > On Wed, 2009-09-23 at 11:30 -0500, Guang Zeng wrote: > > Hi, there, > > > > I have two subjects from two time points, I'd like to compare their > > o

[Freesurfer] how to use mri_compute_seg_overlap

Hi, there, I have two subjects from two time points, I'd like to compare their overlap ratio of FreeSurfer segmented hippocampus. I try to use the command mri_compute_seg_overlap to do it, My command line is: mri_compute_seg_overlap -olog text tp1/mri/aseg.mgz tp2/mri/aseg.mgz Is it correct

Re: [Freesurfer] how to extract segmented hippocampus

, Gonzalo Rojas Costa wrote: > > > Dear Douglas: > > > > And how can I view (render) in 3D the hippocampus that I got frok aseg.mgz > > with the mri_binarize command ?... > > > > Sincerely, > > > > > > Gonzalo Rojas Costa > > > > >

Re: [Freesurfer] tkregister2 question

the same > as case_2, and save the case_1 volume (you can save as 'case_1.nii'). > Then you can use tkregister2. > > Again, without fudicial markers, its difficult to tell left from right, > so there is no guarantee that your l-r orientation is correct. > > Nick >

Re: [Freesurfer] tkregister2 question

s outputs case_2.mat) > > cp case_2.mat case_1.mat > > now tkregister2 should work. Keep in mind this is a hack accounting for > the missing case_1 data. If the data is from different scanners, then > there is a risk of L-R reversal, because the orientation info may not be > t

[Freesurfer] tkregister2 question

Hi, there, I have a case_1.hdr file and case_1.img file, but no the corresponding .mat file which contains the necessary direction cosine info. So everytime when I try to register another nifti file case_2.nii to it using tkregister2 or mri_vol2vol, it always complains that "INFO: could not f

[Freesurfer] hippocampus volume are different after step.3

Hi, there, I ran a subject through FreeSurfer pipeline. I found that the size of left and right hippocampus in aseg.stats are larger than that of left and right hippocampus in wmparc.stats after step. 3. If I want to compare the FreeSurfer segmented hippocampus with a manually traced hippoc

[Freesurfer] how to extract segmented hippocampus

Hi, there, I'd like to extract the left and right hippocampus from aseg.mgz, so basically what I want is a volume where left hippocampus have value (or label) 17 and right hippocampus have value (or label) 53, all the other place are zero. How can I do it? Using mri_threshold or mri_label2vol?

[Freesurfer] longitudinal study

Hi, there, I am going to run the FreeSurfer Longitudinal Stream (FS 4.5) on data from different timepoints. Do we need cross-sectionally process all time points with the default workflow, or just need run the first step of the default workflow. Thanks a lot! Guang ___

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