Re: [Freesurfer] skull strip T2 image in Freesurfer
Hi Bruce and Douglas, After I ran through the FS, I ran the following two commands: bbregister --s T1_0145 --mov T2_0145_file1.nii --reg register.dat --init-fsl --t2 --o outvol mri_vol2vol --mov T1_0145/mri/brain.mgz --reg register.dat --o T1_mappedToT2.nii T1_0145 is the directory for analyzing my T1 image with freesurfer, T2_0145_file1.nii is my T2 image. The result is not good. I am not sure whether there is some problem with my above two commands. Do you have any suggestion? Thanks a lot. Best, Xiaoying 2011/5/23 Xiaoying Tang > I see. > > Thanks a lot. > > > Xiaoying > > 2011/5/22 Bruce Fischl > >> yes, bbregister uses the surfaces generated by recon-all, so run it >> through to the end, then use bbregister. >> >> cheers >> Bruce >> >> On Sun, 22 May 2011, Xiaoying Tang wrote: >> >> Hi Douglas, >>> >>> Thanks for your reply! >>> >>> bbregister succeeded in running now. But I still have another question. >>> >>> You mentioned that "If you have a T1 that you've run through FS".What do >>> you >>> mean by "run through"? I just ran autorecon1 to get the skullstripped T1. >>> Do >>> you mean that I also have to run autorecon2 and autorecon3 if I want to >>> use >>> bbregister? >>> >>> Best, >>> Xiaoying >>> >>> 2011/5/22 Douglas Greve >>> >>> Do you still have version 4.1 in your path? It looks like it is calling an old version of fslregister. doug On 5/22/11 1:26 AM, Xiaoying Tang wrote: Hi Douglas and Bruce, I have updated my freesurfer version to 5.0.0. But I still have error when I tried to run bbregister. The error information is as follows" My command: bbregister --s bert --mov T2_0145_file1.nii --reg register.dat --init-fsl --t2 --o outvol Error information: FREESURFER_HOME /usr/local/freesurfer_versions/freesurfer-centos4_x86_64-v5.0.0 mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii mri_convert T2_0145_file1.nii ./tmp.bbregister.16142/template.nii $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from T2_0145_file1.nii... TR=4162.49, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999276, 0, 0.0380414) j_ras = (-0.00161026, 0.999104, -0.0422986) k_ras = (0.0380073, 0.0423292, 0.998381) writing to ./tmp.bbregister.16142/template.nii... fslregister --s bert --mov ./tmp.bbregister.16142/template.nii --reg ./tmp.bbregister.16142/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.16142/fslregister --dof 6 *ERROR: Flag --niters unrecognized.* I am not sure about the reason since the Flag --niters seems to be created during the process, but not in my original command. I would be most grateful if you could help me solve this problem. Thanks in advance. Best, Xiaoying 2011/5/22 Xiaoying Tang The full name on my machine is: freesurfer-centos4_x86_64-v4.1.0 > > So I think the version is 4.1.0 > > Best, > Xiaoying > > 2011/5/22 Bruce Fischl > > No, it's not the same what version are you running? >> >> >> >> On May 21, 2011, at 11:26 PM, Xiaoying Tang wrote: >> >> Hi Douglas, >> >> Thanks a lot for your suggestion. >> >> It is really strange that I don't find bbregister in the file foler >> of >> the freesurfer on my machine. But I find a program named >> "fslregister". Is >> that the same? >> >> If they are different, is it that I need to update my version of >> freesurfer so that I can have the program bbregister? >> >> Thanks a lot. >> >> Best, >> Xiaoying >> >> 2011/5/21 Douglas Greve >> >> If you have a T1 that you've run through FS and are happy with the >>> skull >>> strip, then you can register your T2 with the FS anatomical (with >>> bbregister), then map the skull stripped T1 into the T2 space >>> (mri_vol2vol), then apply it to the T2 (mri_mask). >>> >>> doug >>> >>> On 5/21/11 7:27 PM, Bruce Fischl wrote: >>> Hi Xiaoying, unfortunately there isn't. I would recommend BET (from the FSL). cheers Bruce On Sat, 21 May 2011, Xiaoying Tang wrote: Hi All, > > I am wondering whether there is any way to skull strip a T2 image > using >>> freesurfer. I tried to use the same way as for skullstripping T1 > image, but >>> always failed. > > I would be most grateful if someone can give me some suggestion. > > Best, > Xiaoying Tang > > > ___ >>> Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.m
Re: [Freesurfer] going between scanner space and freesurfer space
Hi Trina you need to extract the ras2vox matrices from the two volumes, call them R1 and R2 (e.g. from the 001.mgz and the orig.mgz). The transform to take you from voxel coords of one volume to voxel coords of the other is then R1 * inv(R2) cheers Bruce p.s. we do a single interpolation applying the entire affine transform, not sequential ones, which you definitely don't want to do. On Mon, 23 May 2011, Trina Kok wrote: > Hi All, > > We would like to obtain a matrix to go from the orig.mgz/001.mgz space to > freesufer space (i.e. that of T1.mgz, brain.mgz etc). I'm not sure which > combination of vox2ras and ras2vox of the 2 volumes to extract to be able to > obtain say for example, matrix T below. > > [orig.mgz (appended with ones for extra dimension] = T * [T1.mgz (appended > with > ones for extra dimension]; > > On a separate note, I'm using the affine function shown here in the below link > to test out the transformations. The function does the interpolation by > trilinear interpolation, and does rotation, shearing, scaling etc first, and > the translation as a last step. > http://www.mathworks.com/matlabcentral/fileexchange/21080. Is this the same or > almost the same procedure used in going from scanner space to freesurfer > space? > > Thanks a lot! > > Cheers, > Trina > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] going between scanner space and freesurfer space
Hi All, We would like to obtain a matrix to go from the orig.mgz/001.mgz space to freesufer space (i.e. that of T1.mgz, brain.mgz etc). I'm not sure which combination of vox2ras and ras2vox of the 2 volumes to extract to be able to obtain say for example, matrix T below. [orig.mgz (appended with ones for extra dimension] = T * [T1.mgz (appended with ones for extra dimension]; On a separate note, I'm using the affine function shown here in the below link to test out the transformations. The function does the interpolation by trilinear interpolation, and does rotation, shearing, scaling etc first, and the translation as a last step. http://www.mathworks.com/matlabcentral/fileexchange/21080. Is this the same or almost the same procedure used in going from scanner space to freesurfer space? Thanks a lot! Cheers, Trina ___ 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] tksurfer' configure overlay window incomplete...
if the problem is that the 'Apply' button is not visible (which is the case where this screen doesnt fit at smaller resolutions) a workaround is to press the space bar, which does the same thing as pressing 'Apply'. n. On Mon, 2011-05-23 at 15:35 -0400, Krish Subramaniam wrote: > Sorry, this is a known bug. I'll send an email once it's fixed > > Best > Krish > > On May 23, 2011, at 3:21 PM, Gonzalo Rojas Costa wrote: > > > Hi: > > > >I have an ubuntu based computer with Freesurfer 5.0.0, and the > > lowest part of the View->Configure->Overlay window of tksurfer > > didn't appears (see attached image)... How can I correct it ?... The > > PC has 1440x900 of screen resolution... How can I view the complete > > window ?... > > > >In another PC with 1920x1080 of screen resolution, Freesurfer > > 4.5.0 and another Ubuntu version, that tksurfer window looks ok (see > > atached image)... > > > >Sincerely, > > > > > > Gonzalo Rojas Costa > > Laboratory for Advanced Medical Image Processing > > Department of Radiology > > Las Condes Clinic > > Lo Fontecilla 441, Las Condes, Santiago, Chile. > > Tel: 56-2-2105170 > > Cel: 56-9-97771785 > > www.clc.cl > > > > > > < > > Screenshot > > -4 > > .jpg>___ > > 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] tksurfer' configure overlay window incomplete...
Sorry, this is a known bug. I'll send an email once it's fixed Best Krish On May 23, 2011, at 3:21 PM, Gonzalo Rojas Costa wrote: > Hi: > >I have an ubuntu based computer with Freesurfer 5.0.0, and the > lowest part of the View->Configure->Overlay window of tksurfer > didn't appears (see attached image)... How can I correct it ?... The > PC has 1440x900 of screen resolution... How can I view the complete > window ?... > >In another PC with 1920x1080 of screen resolution, Freesurfer > 4.5.0 and another Ubuntu version, that tksurfer window looks ok (see > atached image)... > >Sincerely, > > > Gonzalo Rojas Costa > Laboratory for Advanced Medical Image Processing > Department of Radiology > Las Condes Clinic > Lo Fontecilla 441, Las Condes, Santiago, Chile. > Tel: 56-2-2105170 > Cel: 56-9-97771785 > www.clc.cl > > > < > Screenshot > -4 > .jpg>___ > 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] question abt fsaverage V1
that V1 label is produced as part of the Brodmann area set that is produced by default in recon-all. those labels are described here: https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps the Hind's V1 must be run separately, by running: recon-all -s subjid -label-v1 n. On Mon, 2011-05-23 at 10:35 -0400, Ritobrato Datta wrote: > Hello All, > > I noticed that that there is a fsaverage/label/?h.V1.label > > Is this label created from the Hinds and Fischl method ? Can someone give > some details abt it ? > > Also for individual subjects, when I run the V1 estimation using Hinds and > Fischl method, how accurate are the V1 / V2 border compared to retinotopy ? > Or which is more accurate ? > > Thanks > > Ri > ___ > 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] fMRI data from FSL into Freesurfer: is my workflow correct?
Dear Doug, Thank you again very much for your help. I am replying with a delay because I was travelling. Please see my questions& comments below in the text: On 5/10/11 5:48 PM, "Douglas N Greve" wrote: > > > Agnieszka Burzynska wrote: >> Dear Doug, >> Thank you a lot for your reply! >> >> Yes, I did use reg-feat2anat and registered example_func to the subject's >> anatomical. As far as I understand it, then the registration matrix can be >> used for a contrast of interest. >> >> That's great news that the software version will not be a problem. >> >> I will use the copes, thank you. >> >> My cope images have a range of, for example, -500 to 500 with the peak at 0. >> When I view them on the subject anatomical in the freesurfer >> >> (with command tkmedit 1109 orig.mgz lh.white -aux brain.mgz -overlay >> ./run1.feat/stats/cope1.nii.gz -overlay-reg >> ./run1.feat/reg/freesurfer/anat2exf.register.dat -segmentation >> aparc+aseg.mgz -fthresh 2.3 -fmax 4.3 >> ), >> >> the -fthresh 2.3 and -fmax 4.3 are not suitable. However, when I try to >> adjust the threshold in View/Configure/Functional Overlay I get this error >> message: >> >> Invalid values. >> Tkmedit couldn't set the threshold to the values you specfied. Please make >> sure the minimum is less than or equal to the midpoint, and the slope is >> greater than 0. >> > What are you trying to adjust them to? I tried to apply some meaningful threshold, otherwise the whole brain is yellow-blue. However, so far the zstats (as you refer to them bewlo) look ok, so I may use zstats, given our later analyses. >> I am not sure how to deal with this. >> >> Now the last point: >> - I will want to create a fMRI-based ROI and then investigate the thickness especially within this region. i know I can extract mean ROI values and use other statistical software, but how can I perform vertex-wise analysis within this ROI? I assume qdec does not allow this, so only the DODDS analysis is possible. >>> Which stat map do you want to derive the ROI from? The group map? >>> >> >> Yes, my first idea was to create a conjunction image across all subjects, >> specify the ROI on the fsaverage, then map this ROI back to subjects' >> individual surfaces. And then see whether across subjects, thickness is >> related to fmri data within this cortical patch. >> > If you are going to create a conjunction, then you should use the > zstats. But then you have another problem in that the zstats are going > to be very low because no smoothing was done. But if you're happy with > the maps, then go for it. Alternatively, you can do a group analysis of > the copes and then threshold the sig maps. In either case, the map will > be in the fsaverage space. You can create a label in tksurfer. Then run > mri_preproc to get all of your subjects thickness files into one file in > fsaverage space. Then run mri_segstats using the --slabel and --avgwf > options with the thickness file as input. The avgwf file will be a list > of thicknesses for each subject averaged over the ROI. > > doug I plan to apply smoothing on the surface when averaging the 3 runs for each subjects, so I hope zstats will look sufficiently good (I am still checking it). Concerning the ROI issue, if possible, I would NOT do the ROI-analysis. Instead, I am searching for a way to correlate the thickness with fMRI data across subjects (both data types are in fsaverage space). In other words, I have two images for each subject in the surface space: the thickness and some fmri measure. I would like to see how they are related vertex-wise within some larger regions of interest. It would be great if you could give me some guidance here, as I cannot find the solution in the archives or the tutorials. With best greetings, Aga >> Thank you again for your help! >> Cheers, >> Aga >> >> On 5/10/11 4:39 PM, "Douglas N Greve" wrote: >> >> >>> Hi Aga, comments below >>> >>> Burzynska, Aga wrote: >>> Dear all, I just wanted to double-check if I am doing the right thing. I am transferring fMRI data from FSL to the surface in Freesurfer to test whether cortical thickness is related to BOLD signal change. I used the steps described here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer I did the following: 1) I carried out Freesurfer reconstruction for all subjects 2) I performed 1st level analysis for fMRI data in FSL, separately for each run, without smoothing 3) Then I obtained good registration of FEAT example_func of each run to the subject's anatomical using FLIRT. This I have done already for a specific contrast of interest. >>> Did you not use reg-feat2anat for this step? Did you register the z-map >>> itself? If so, that is not the right thing to do, it should be the >>> example_func. >>> The above steps have been performed
Re: [Freesurfer] question abt fsaverage V1
Hi Ri it depends on how you do the retinotopy (field strength, # of coil elements, voxel size, etc). In our comparisons, the folding patterns predict the border location to about 2.5mm, which is probably better than you can get with retinotopy. I believe the ?h.V1.label comes from the Zilles/Amunts histological data, and should be mostly equivalent to the Hinds stuff. cheers Bruce On Mon, 23 May 2011, Ritobrato Datta wrote: > Hello All, > > I noticed that that there is a fsaverage/label/?h.V1.label > > Is this label created from the Hinds and Fischl method ? Can someone give > some details abt it ? > > Also for individual subjects, when I run the V1 estimation using Hinds and > Fischl method, how accurate are the V1 / V2 border compared to retinotopy ? > Or which is more accurate ? > > Thanks > > Ri > ___ > 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] Running FreeSurfer Remotely
I run it using NX for windows all the time. I assume is works on OSX as well. cheers Bruce On Mon, 23 May 2011 obre...@nmr.mgh.harvard.edu wrote: > Hi, > > Will FreeSurfer run remotely using NX Client for OSX or should I employ > VNC only? > > Thanks, > > Gabriel > ___ > 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] Running FreeSurfer Remotely
It will probably work. However the experience can be sluggish On Mon, May 23, 2011 at 11:34, wrote: > Hi, > > Will FreeSurfer run remotely using NX Client for OSX or should I employ > VNC only? > > Thanks, > > Gabriel > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] question abt fsaverage V1
Hello All, I noticed that that there is a fsaverage/label/?h.V1.label Is this label created from the Hinds and Fischl method ? Can someone give some details abt it ? Also for individual subjects, when I run the V1 estimation using Hinds and Fischl method, how accurate are the V1 / V2 border compared to retinotopy ? Or which is more accurate ? 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.
[Freesurfer] Running FreeSurfer Remotely
Hi, Will FreeSurfer run remotely using NX Client for OSX or should I employ VNC only? Thanks, Gabriel ___ 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] loading qdec.table.dat error
Ok, now everything works. I just opened the file in terminal using pico and saved it. On Mon, May 23, 2011 at 9:43 AM, Tetiana Dadakova wrote: > Thank you Nick, > > Now I have another error: > > Loading data table > /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat... > Number of columns: 384 > fsid column: 1 > Number of factors: 383 > Number of subjects: 0 > ERROR: QdecDataTable::Load: number of subjects = 0 > Error loading the data table. > > Although there are just 3 columns and 126 subjects.Maybe I do > something wrong when creating the file, therefore here are my steps: > 1. Create table it in MS Excel, save it as tab-delimited qdec.table.txt > 2. Open qdec.table.txt and end one carriage return in the end to > prevent problem described above > 3. change .txt into .dat > > Am I doing something wrong? > > Thanks, > Tanja. > > > On Sat, May 21, 2011 at 6:09 PM, Nick Schmansky > wrote: >> I think you might need to add an extra carriage return at the end of the >> last line. in other words, your cursor should go an empty line at the >> bottom of the file. >> >> n. >> >> >> >> On Sat, 2011-05-21 at 14:34 +0200, Tetiana Dadakova wrote: >>> Dear list, >>> >>> I am trying to load qdec.table.dat file using qdec, and get the following >>> error: >>> >>> Loading data table >>> /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat... >>> QdecDataTable::Load: will attempt to open as Mac text file... >>> Number of columns: 3 >>> fsid column: 1 >>> Number of factors: 2 >>> Number of subjects: 126 >>> ERROR: QdecDataTable::Load: problem parsing file >>> /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat >>> This line did not appear to end with a newline: >>> PAT_ViOl 25 pat >>> Error loading the data table. >>> >>> This is the last line in the file and therefore there is no new line after >>> it. >>> What can cause this error? >>> >>> Thank you, >>> Tanja. >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] loading qdec.table.dat error
Thank you Nick, Now I have another error: Loading data table /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat... Number of columns: 384 fsid column:1 Number of factors: 383 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. Although there are just 3 columns and 126 subjects.Maybe I do something wrong when creating the file, therefore here are my steps: 1. Create table it in MS Excel, save it as tab-delimited qdec.table.txt 2. Open qdec.table.txt and end one carriage return in the end to prevent problem described above 3. change .txt into .dat Am I doing something wrong? Thanks, Tanja. On Sat, May 21, 2011 at 6:09 PM, Nick Schmansky wrote: > I think you might need to add an extra carriage return at the end of the > last line. in other words, your cursor should go an empty line at the > bottom of the file. > > n. > > > > On Sat, 2011-05-21 at 14:34 +0200, Tetiana Dadakova wrote: >> Dear list, >> >> I am trying to load qdec.table.dat file using qdec, and get the following >> error: >> >> Loading data table >> /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat... >> QdecDataTable::Load: will attempt to open as Mac text file... >> Number of columns: 3 >> fsid column: 1 >> Number of factors: 2 >> Number of subjects: 126 >> ERROR: QdecDataTable::Load: problem parsing file >> /Applications/freesurfer/subjects/group_analysis/qdec/qdec.table.dat >> This line did not appear to end with a newline: >> PAT_ViOl 25 pat >> Error loading the data table. >> >> This is the last line in the file and therefore there is no new line after >> it. >> What can cause this error? >> >> Thank you, >> Tanja. >> ___ >> 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
