Re: [Freesurfer] QDEC Alternative

External Email - Use Caution no plans for a new gui. you might look up qdecr. this is a 3rd party altenative that uses R; I've never used it myself, so I don't know how well it works on voxel-wise analysis or if there is a gui On 5/1/2023 2:00 PM, Lauren Stephens wrote:   

Re: [Freesurfer] Qdec: Can't find a usable init.tcl

External Email - Use Caution Hello Rosa, The qdec program is deprecated in 7.X releases and is no longer maintained. In the 7.X releases, you can try using freeview for images and from the command line there are the mri* commands (mris_surf2surf, mri_glmfit, mri_glmfit-sim, etc.)

Re: [Freesurfer] qdec analysis error

Sorry, we are not supporting qdec anymore. You will need to use the command-line stream On 3/23/2022 8:02 AM, David wrote: External Email - Use Caution Hello FreeSurfer Developers, I have a problem. Can you help me freesurfer version : 6.0.0 Load qdec when I run qdec.table.dat, the

Re: [Freesurfer] Qdec error

We are not supporting qdec anymore. Try using the "command line stream", ie, mris_preproc, FSGD, etc On 12/1/2021 6:47 PM, Arian Klows wrote: External Email - Use Caution  Dear FS experts, I have freesurfer-linux-centos7_x86_64-7.1.1 on my computer and when I run qdec, I get the fol

Re: [Freesurfer] QDEC command not found

We are no longer supporting qdec On 9/21/2021 2:15 PM, Fabiola Macruz wrote: External Email - Use Caution External Email - Use Caution Dear freesurfer experts, I have installed the freesurfer version 7.1.1 in my computer (Mac). After running the longitudinal pipeline in all th

Re: [Freesurfer] Qdec vertex-wise clustering question

I think i'm misunderstanding your question. Typically, you are running the stats on the thickness, so of course anything that changes thickness would impact the stats. Am I missing something? On 7/15/2021 2:34 PM, Alejandro Meruelo wrote: > External Email - Use Caution > > I see, thank

Re: [Freesurfer] Qdec vertex-wise clustering question

External Email - Use Caution I see, thank you. Would statistics on cortical thickness calculations be impacted? Many thanks again, Alejandro On Thu, Jul 15, 2021 at 8:38 AM Douglas N. Greve wrote: > > if you are doing statistics on the surface measures, then they will > impact t

Re: [Freesurfer] Qdec vertex-wise clustering question

if you are doing statistics on the surface measures, then they will impact the calculations On 7/14/2021 7:07 PM, Alejandro Meruelo wrote: > External Email - Use Caution > > This is very helpful, thank you! Do the recon-all generated FreeSurfer > data (e.g., surfaces) impact any of the s

Re: [Freesurfer] Qdec vertex-wise clustering question

External Email - Use Caution This is very helpful, thank you! Do the recon-all generated FreeSurfer data (e.g., surfaces) impact any of the statistical calculations or are they primarily used for figure generation for Qdec? Many thanks again, Alejandro On Mon, Jul 12, 2021 at 6:2

Re: [Freesurfer] Qdec vertex-wise clustering question

Not sure I know what you mean. For creating the design matrix, it uses the info from the qdec table. BTW, qdec is deprecated. On 7/12/2021 5:27 PM, Alejandro Meruelo wrote: > External Email - Use Caution > > Hello, > > I had a brief question regarding Qdec vertex-wise clustering. Does >

Re: [Freesurfer] QDEC/mri_glmfit questions

You can't do it in tandem. The 2nd command should work, just don't include -surf or -label Also, when you do use -surf, you need a subject and a hemi, eg, -surf fsaverage lh On 2/24/2021 12:03 PM, Erin Moe wrote: > External Email - Use Caution > > Hi Doug, > Thank you for the advice! I

Re: [Freesurfer] QDEC/mri_glmfit questions

External Email - Use Caution Hi Doug, Thank you for the advice! I tried plugging the output of aparc2stats into mri_glmfit both in tandem with —y (mri_preproc_output).mgh as well as on its own and got an error message from mri_reshape saying the elements cannot be changed nv1=16

Re: [Freesurfer] QDEC/mri_glmfit questions

It might be easiest to start with running the ROI values in mri_glmfit. How did you extract the ROI values for use in SPSS? You can use aparcstats2table to create a table, and then feed that table into mri_glmfit --table table.dat --o glmdir —fsgd inflammatory_markers.fsgd —C Inflammatory_group.

Re: [Freesurfer] Qdec crash while analysis almost finished

ter I downloaded different versions(v5.3,v6.0,v7.1). So I think using which one is OK maybe. Chan -原始邮件- 发件人:"Greve, Douglas N.,Ph.D." 发送时间:2021-01-15 00:05:53 (星期五) 收件人: "freesurfer@nmr.mgh.harvard.edu" 抄送: 主题: Re: [Freesurfer] Qdec crash while analysis almost

Re: [Freesurfer] Qdec crash while analysis almost finished

I'm not sure I understand. Are you using v6 qdec with a 5.3 license file? On 1/13/2021 2:54 AM, chenb...@mail.sysu.edu.cn wrote: External Email - Use Caution Hi, dear Freesurfer experts, I recently came across an invalid Freesurfer license key error w

Re: [Freesurfer] qdec replacement

We don't have a GUI, if that is what you mean. The default now is to use the command line stream where you create your own FSGD file and contrast matricies, then run mri_glmfit and mri_glmfit-sim On 11/17/2020 10:44 AM, Pagliaccio, David (NYSPI) wrote: ___

Re: [Freesurfer] Qdec - talairach to vertex for display purposes

We don't use qdec anymore, so I can't remember what the interface is like. You can transfer your coordinates to fsaverage space, see https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems and then go to that point in freeview On 10/13/2020 9:45 AM, Paul Dhami wrote: External Ema

Re: [Freesurfer] qdec problems not receiving keyboard input

Sorry, qdec has been mothballed and we are not supporting it anymore On 10/7/2020 7:12 AM, Agurne Sampedro Calvete wrote: External Email - Use Caution Dear Freesurfer Experts, Although I haven't had any problems with the qdec until now, this week the qdec is having some errors when r

Re: [Freesurfer] QDEC command not found

We are no longer distributing or supporting qdec On 10/2/2020 6:17 AM, Enrico Collantoni wrote: External Email - Use Caution Dear freesurfer experts, I installed the 7.1.1 version of freesurfer in iOS enviroment (10.15.4). I could run the recon-all without any problems. However, tryin

Re: [Freesurfer] QDEC analyses

esurfer"; *Subject:* Re: [Freesurfer] QDEC analyses How you did you do your analysis? As an exploratory/map-based analysis? Or as an ROI analysis? How did you correct for multiple comparisons? Generally, in a map-based analysis, the correction for multiple comparisons incorporates the fact that ther

Re: [Freesurfer] QDEC analyses

External Email - Use Caution Thanks for your timely response. To assess the two group differences in cortical thickness, whole-brain vertex-wise analyses were performed using the graphical user interface of FreeSurfer known as QDEC. We used a general linear model to compare the

Re: [Freesurfer] QDEC analyses

External Email - Use Caution Thanks for your timely response.  To assess the two group differences in cortical thickness, whole-brain vertex-wise analyses were performed using the graphical user interface of FreeSurfer known as QDEC. We used a general linear model to compare the

Re: [Freesurfer] QDEC analyses

How you did you do your analysis? As an exploratory/map-based analysis? Or as an ROI analysis? How did you correct for multiple comparisons? Generally, in a map-based analysis, the correction for multiple comparisons incorporates the fact that there are two hemispheres being tested. On 6/20/

Re: [Freesurfer] QDEC correlation analysis

In the qdec  output, there should be a file called Xg.dat and one called contrast/C.dat (where contrast is the name of the contrast of interest) X = load('Xg.dat'); C = load('contrast/C.dat'); y = MRIread('input-to-qdec.mgz'); % Not sure what this is called ymat = fast_vol2mat(y); yvertex = yma

Re: [Freesurfer] QDEC error Two Groups three covariates

Sorry, one of the reasons we stopped supporting QDEC was because it became impossible to debug these kinds of things. Please use the command line stream (ie, create an FSGD file and contrast matrices, run mris_preproc, mris_fwhm, and mri_glmfit). I can help you once you recreate the error On

Re: [Freesurfer] qdec and mris_anatomical_stats help

On 5/15/2020 8:17 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caution Dear Freesurfer experts, Hope everyone is doing well! Could someone please clarify some things about mris_anatomical_stats, done afte

Re: [Freesurfer] qdec and mris_anatomical_stats help

External Email - Use Caution Hello Freesurfer experts, Just wanted to follow-up from my last email. If any clarification is needed regarding what I'm trying to understand from mris_anatomical_stats, please let me know! Kind regards, Alex On Fri, May 15, 2020 at 8:17 PM Lab of Aut

Re: [Freesurfer] Qdec not running ("image not found" error message)

External Email - Use Caution Hello Alex, It looks like you need to install Xquartz on your Mac with the X Windows libraries including libGLU.1.dylib. Download from here, open and run the installer package. https://www.xquartz.org/ - R. On Feb 25, 2020, at 23:27, Lab of Autism and

Re: [Freesurfer] qdec / tksurfer GUI

Have you tried freeview? On 2/7/2020 2:50 PM, Rockers, Elijah D. wrote: External Email - Use Caution I've noticed an issue when trying to manually input values into fields with Qdec. This problem has been reported before. I thought perhaps it was because Qdec is deprecated, so I load

Re: [Freesurfer] Qdec error

I would normalize all the variables. Eg, column 2 is nearly identical to column 1 On 1/22/2020 1:03 AM, vittal korann wrote: External Email - Use Caution Dear Douglas I did normalize ICV values. This is something else I guess. With regards Vittal On Tue, Jan 21, 2020 at 6:09 PM vit

Re: [Freesurfer] Qdec and TkSurfer input boxes

I don't know. Can you reconfigure to English to do a test? On 1/21/2020 12:14 PM, Marcos Martins da Silva wrote: External Email - Use Caution FreeSurfer 6 over CentOS 7. I have the same problem with 5.3 too. One more information: CentOS 7 is configured as PT-br instead of English. Could

Re: [Freesurfer] Qdec error

External Email - Use Caution Dear Douglas I did normalize ICV values. This is something else I guess. With regards Vittal On Tue, Jan 21, 2020 at 6:09 PM vittal korann wrote: > Dear FreeSurfer experts > > I ran QDEC and got the following error. > > Design matrix

Re: [Freesurfer] Qdec and TkSurfer input boxes

External Email - Use Caution FreeSurfer 6 over CentOS 7. I have the same problem with 5.3 too. One more information: CentOS 7 is configured as PT-br instead of English. Could it be the reason? Em ter, 21 de jan de 2020 12:29, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> escre

Re: [Freesurfer] Qdec error

Try normalizing your covariates (ie, remove the mean and divide by the stddev) On 1/21/2020 7:39 AM, vittal korann wrote: External Email - Use Caution Dear FreeSurfer experts I ran QDEC and got the following error. Design matrix -- 1.0 1.04000 -1.38574 2.0

Re: [Freesurfer] Qdec and TkSurfer input boxes

Which version of FS are you using? I don't have this problem in v6 or dev. What OS are you using? On 1/17/2020 9:09 AM, Marcos Martins da Silva wrote: External Email - Use Caution Thank you, Doug! Yes, there is an option to load a fsgd file in Freeview, but when you try to use this op

Re: [Freesurfer] Qdec and TkSurfer input boxes

External Email - Use Caution Thank you, Doug! Yes, there is an option to load a fsgd file in Freeview, but when you try to use this option Freeview closes wirh error. I tried to use the y.fsgd generated by Qdec process. This file works great when you use it in TkSurfer, but not in

Re: [Freesurfer] Qdec and TkSurfer input boxes

Sorry, qdec and tksurfer are becoming (have become?) obsolete. I think you can load an fsgd file in freeview On 1/15/2020 11:02 AM, Marcos Martins da Silva wrote: External Email - Use Caution Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with input/entry/edit box

Re: [Freesurfer] Qdec support {Disarmed}

External Email - Use Caution Hello Leona, What is the error that you are seeing? Qdec is a 32 bit program (*not* 64 bit), so even Mac OS 10.14 (Mojave) may put up a warning that it is not optimized and needs to be re-compiled, but it should still run.  It will not however run if

Re: [Freesurfer] QDEC cluster output

Hi Lara, sorry, we don't really support qdec anymore for the very reason that we can't get into the code easily and answer these questions. Can you use the command-line stream? doug On 10/17/19 6:17 PM, Lara Foland-Ross wrote: External Email - Use Caution Hi Freesurfer experts, I’m ru

Re: [Freesurfer] qdec contrast and data extraction

t;// > >/Which specific file should I load? I see cluster.mgh, > cluster.summary, sign.ocn.annot, sig.ocn.mgh, sig.vertex.mgh, and > pdf.dat./ > >// > >/How can I extract the values from fsaverage space?/ > >// > >/Basically, what is the correct

Re: [Freesurfer] qdec contrast and data extraction

to extract values from these significant > clusters? > > Many thanks, > Omar > > Date: Tue, 3 Sep 2019 15:15:02 + > From: "Greve, Douglas N.,Ph.D." mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> &g

Re: [Freesurfer] qdec contrast and data extraction

t; > Basically, what is the correct way to extract values from these significant > clusters? > > Many thanks, > Omar > > Date: Tue, 3 Sep 2019 15:15:02 + > From: "Greve, Douglas N.,Ph.D." > Subject: Re: [Freesurfer] qdec contrast and data extrac

Re: [Freesurfer] qdec contrast and data extraction

You might have done something wrong along the way. When you run the montecarlo correction, it will create a file with the thickness values in it for each cluster. the first thing to do is to load that and see if you see the expected differences. The other thing is to not go back into native spac

Re: [Freesurfer] Qdec Message to Mailing List

<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Qdec Message to Mailing List can you send the command line, full terminal output, your fsgd file, and the Xg.dat created in the output? On 7/3/2019 11:05 AM, Marie Hill wrote: External Email - Use Caution Thanks. When I ru

Re: [Freesurfer] Qdec Message to Mailing List

rfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu> Sent: 03 July 2019 16:22 To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Qdec Message to Mailing List can you send the command line, full te

Re: [Freesurfer] Qdec Message to Mailing List

) ... could not determine the cause of the problem Kind Regards, Marie From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: 03 July 2019 16:22 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec Message to Mailing

Re: [Freesurfer] Qdec Message to Mailing List

mgh.harvard.edu> Sent: 03 July 2019 15:24 To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Qdec Message to Mailing List yes, qdec can only have 2 factors with 2 levels. both qdec and mri_glmfit are linear methods (in fact, qdec just calls m

Re: [Freesurfer] Qdec Message to Mailing List

of Greve, Douglas N.,Ph.D. Sent: 03 July 2019 15:24 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Qdec Message to Mailing List yes, qdec can only have 2 factors with 2 levels. both qdec and mri_glmfit are linear methods (in fact, qdec just calls mri_glmfit). On 7/3/2019 9:39 AM

Re: [Freesurfer] Qdec Message to Mailing List

yes, qdec can only have 2 factors with 2 levels. both qdec and mri_glmfit are linear methods (in fact, qdec just calls mri_glmfit). On 7/3/2019 9:39 AM, Marie Hill wrote: External Email - Use Caution Dear Sir/Madam, Could I post the following message to the mailing list: I am running

Re: [Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

Hi Arsenije, the file name should be (with a starting “.” and no file extension): $SUBJECTS_DIR/qdec/.Qdecrc Best, Martin > On 22. Feb 2019, at 00:22, Arsenije Subotic > wrote: > > Dear Freesurfer experts, > > I am having issues choosing the spc option for my QDEC two stage longitudinal

Re: [Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

qdec is not really being supported anymore. It is better if you use the command line stream On 2/21/19 6:22 PM, Arsenije Subotic wrote: External Email - Use Caution Dear Freesurfer experts, I am having issues choosing the spc option for my QDEC two stage longitudinal analysis as it

Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

They are the same thing underneath. On 10/18/18 11:12 AM, Azeez, Azeezat wrote: External Email - Use Caution Thank you for the response. Which smoothing option would you recommend, there is one in mris_preproc, but there is also mris_smooth. Thanks You On Wed, Oct 17, 2018 at 1:56 PM G

Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

External Email - Use Caution Thank you for the response. Which smoothing option would you recommend, there is one in mris_preproc, but there is also mris_smooth. Thanks You On Wed, Oct 17, 2018 at 1:56 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > You cannot use Q

Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

You cannot use QDEC for this. You must use the "command line" stream, ie, create your FSGD file, run mris_preproc, smooth, run mri_glmfit, then mri_glmfit-sim. See the tutorial on the wiki. On 10/17/2018 01:30 PM, Azeez, Azeezat wrote: > > External Email - Use Caution > > Hello, > > I wo

Re: [Freesurfer] qdec analysis with more than 2 covariates

That looks like the terminal output for qdec. You cannot use qdec with your design. If you have questions about the FSGD, I'll be happy to answer them. On 10/16/2018 11:00 AM, vittal korann wrote: > > External Email - Use Caution > > Hi Doug, > > Thank you for your response. > I tried th

Re: [Freesurfer] qdec analysis with more than 2 covariates

External Email - Use Caution Hi Doug, Thank you for your response. I tried the link which you sent yesterday. But got stuck while creating qdec.fsgd file. Below i have pasted the terminal output after loading the data. 1 Left-Lateral-Ventricle continuous 0 2 Left-Inf-Lat-Vent

Re: [Freesurfer] qdec analysis with more than 2 covariates

You cannot use QDEC. For this case you'll need to use the "command line" stream. You'll need to start by creating an FSGD file https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples On 10/15/18 10:15 AM, vittal korann wrote: External Email - Use Caution Hi Doug, Recently I started work

Re: [Freesurfer] QDEC, order of groups for interpretation of results

I'm pretty sure that is uses the order in the .levels file. It will create a y.fsgd file in the output folder. Look at the order in that as that will be definitive. On 5/29/18 2:15 PM, Avi Gharehgazlou wrote: Hello experts, I am using QDEC to compared LGI values between groups (typically

Re: [Freesurfer] QDEC, order interpretationof Gracias @batmarandua for aqaa

External Email - Use Caution On Tue, May 29, 2018, 20:16 Avi Gharehgazlou wrote: > External Email - Use Caution > > Hello experts, > > I am using QDEC to compared LGI values between groups (typically develping > and ASD). I made a "diagnosis.levels" file, putting my 2 gro

Re: [Freesurfer] QDEC vs. Command Line Stream

They both give the same results for the same analysis. It is harder to do proper correction for multiple comparisons in QDEC On 4/20/18 12:50 PM, Arsenije Subotic wrote: Dear experts, I'm about to start my cortical thickness analysis for my groups, and I was just wondering what seems to b

Re: [Freesurfer] QDEC Interaction of Two Covariates

QDEC is mostly depreicated. Use the command-line stream. See the group analysis on this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial On 04/19/2018 04:48 PM, David S Lee wrote: > > > Hi FreeSurfer Experts, > > I want to test the relationship between cortical thickness and two > cont

Re: [Freesurfer] QDEC Set Up

Yes, that is the same On 02/12/2018 07:15 PM, Martin Juneja wrote: > Since I have 4 groups here: X1-M, X2-M, X1-F and X2-F, so can someone > please confirm if this is identical to this example: > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V > If so, then I can follow instructions on this

Re: [Freesurfer] QDEC Set Up

Since I have 4 groups here: X1-M, X2-M, X1-F and X2-F, so can someone please confirm if this is identical to this example: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V If so, then I can follow instructions on this page and set up my contrast files accordingly. Thanks. On Mon, Feb 12, 2018

Re: [Freesurfer] qdec question

If you are asking whether you can mix versions of FS, the answer is no. You should analyze all your data using a single version. On 12/30/17 3:27 AM, Giovanni de Marco wrote: Hello, I’ve got a question concerning qdec running with freesurfer. I just downloaded the latest version of freesurfe

Re: [Freesurfer] Qdec Table Loading Error

ber 14, 2017 9:47:54 AM > *To:* Arsenije Subotic > *Subject:* Re: [Freesurfer] Qdec Table Loading Error > The table is not quite the right format. Your first line is > > > lh.aparc.thickness  lh_MeanThickness_thickness > BrainSegVolNotVent  eTIV    gender  age > > >

Re: [Freesurfer] Qdec Table Loading Error

can you send the table? On 12/12/2017 01:18 PM, Arsenije Subotic wrote: > > Dear experts, > > > I'm currently trying to import some of my data into Qdec in order to > perform a group analysis on cortical thickness. All of my data was > originally in an excel sheet and it had the following varia

Re: [Freesurfer] QDEC and comparing two conditions

If you want to do a conjunction, you can run mri_concat with the --conjunct option (see --help for more details). If you want to look at simple overlap, you can threshold each sig map (mri_binarize), then combine them together something like fscalc map2.bin.nii.gz mul 2 add map1.bin.nii.gz -o o

Re: [Freesurfer] QDEC and comparing two conditions

hmmm, it might be easiest to do at least some of this in matlab cheers Bruce On Thu, 30 Nov 2017, Rizvi, Batool wrote: Hi – I’m still wondering what would be the best method to perform the mentioned steps. Additionally, would mri_compute_overlap provide output related to spatial overlap and

Re: [Freesurfer] QDEC and comparing two conditions

Hi - I'm still wondering what would be the best method to perform the mentioned steps. Additionally, would mri_compute_overlap provide output related to spatial overlap and difference, that we're looking for? Is it possible to do this with thickness, or maybe not - because it doesn't consider ar

Re: [Freesurfer] Qdec

I get it. Thank you very much. Best, Zheng At 2017-11-27 11:46:46, "Bruce Fischl" wrote: It’s because people have found empirically that surface area and volume are correlated with TIV, but thickness is not cheers Bruce On Nov 26, 2017, at 9:54 PM, 郑凤莲 <13181786...@163.com> wrote: Hi

Re: [Freesurfer] Qdec

It’s because people have found empirically that surface area and volume are correlated with TIV, but thickness is not cheers Bruce > On Nov 26, 2017, at 9:54 PM, 郑凤莲 <13181786...@163.com> wrote: > > Hi Bruce, > > Thanks for your help. But I have a doubt in why we should do in this way? > Ar

Re: [Freesurfer] Qdec

Hi Bruce, Thanks for your help. But I have a doubt in why we should do in this way? Are there any principles or mechanisms in Qdec? Sincerely, Zheng At 2017-11-27 10:47:49, "Bruce Fischl" wrote: Yes On Nov 26, 2017, at 9:40 PM, 郑凤莲 <13181786...@163.com> wrote: Hi Bruce, Tha

Re: [Freesurfer] Qdec

Yes > On Nov 26, 2017, at 9:40 PM, 郑凤莲 <13181786...@163.com> wrote: > > Hi Bruce, > That is, I should set eTIV at Nuisance Factors for volume and surface > area, not for thickness in qdec, is it right? > > > > > > At 2017-11-27 10:22:05, "Bruce Fischl" wrote: > >you should correct for

Re: [Freesurfer] Qdec

Hi Bruce, That is, I should set eTIV at Nuisance Factors for volume and surface area, not for thickness in qdec, is it right? At 2017-11-27 10:22:05, "Bruce Fischl" wrote: >you should correct for eTIV for volume (but not for thickness) >On Mon, 27 >Nov 2017, 郑凤莲 wrote: > >> Hi Greve,

Re: [Freesurfer] Qdec

you should correct for eTIV for volume (but not for thickness) On Mon, 27 Nov 2017, 郑凤莲 wrote: Hi Greve,     Only for age and surface area, no thickness or volume, is it right? Thanks! Zheng At 2017-11-26 03:04:26, "Douglas Greve" wrote: Yes, for age and surface area. On 1

Re: [Freesurfer] Qdec

Hi Greve, Only for age and surface area, no thickness or volume, is it right? Thanks! Zheng At 2017-11-26 03:04:26, "Douglas Greve" wrote: Yes, for age and surface area. On 11/23/17 2:05 AM, 郑凤莲 wrote: Hi professors, I am using Qdec in Freesurfer. I want to study the re

Re: [Freesurfer] Qdec

Yes, for age and surface area. On 11/23/17 2:05 AM, 郑凤莲 wrote: Hi professors,     I am using Qdec in Freesurfer. I want to study the relationships between age and cortical thickness, age and cortical volume, age and surface area. Is it necessary to corrected by eTIV for volume and surface ar

Re: [Freesurfer] QDEC

: "freesurfer@nmr.mgh.harvard.edu" Betreff: Re: [Freesurfer] QDEC No idea. Can you send the file? On 11/9/17 12:42 PM, Kinzel, Phillipp wrote: Hi Doug, do you have any other ideas why I can´t open the project file? Best, Philipp Von: <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

Re: [Freesurfer] QDEC

2017 um 14:33 *An: *Freesurfer support list *Betreff: *Re: [Freesurfer] QDEC Hi Douglas, thank you for your quick response. Yes, I have permission to read and write for the file. I modified the permission to be able to execute the file as well, but that didn´t change anything. I created the fi

Re: [Freesurfer] QDEC

Hi Doug, do you have any other ideas why I can´t open the project file? Best, Philipp Von: im Auftrag von "Kinzel, Phillipp" Antworten an: Freesurfer support list Datum: Mittwoch, 8. November 2017 um 14:33 An: Freesurfer support list Betreff: Re: [Freesurfer] QDEC Hi Douglas,

Re: [Freesurfer] QDEC

. Von: im Auftrag von Douglas Greve Antworten an: Freesurfer support list Datum: Mittwoch, 8. November 2017 um 09:51 An: "freesurfer@nmr.mgh.harvard.edu" Betreff: Re: [Freesurfer] QDEC Do you have permission to read it? How was it created? On 11/8/17 1:18 AM, Kinzel, Phillipp wrote:

Re: [Freesurfer] QDEC

Do you have permission to read it? How was it created? On 11/8/17 1:18 AM, Kinzel, Phillipp wrote: Hi, I have problems loading project  files in QDEC. I get the following error: Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qd

Re: [Freesurfer] Qdec result

They might be very similar if there is not effect of genotype or the effect is orthogonal to age. On 10/30/2017 03:39 AM, hiroki.s...@med.tohoku.ac.jp wrote: > Dear experts > > I'm using Qdec. > I want to check regions where age and thickness are correlated, and > regions where the thickness-age

Re: [Freesurfer] Qdec image considering multiple variables

Not in FS, sorry. On 10/13/17 3:59 AM, 박경일 wrote: So, I'm wondering if there is another way to draw statistical map considering multiple factors including missing variables. Thanks a lot. Kyung 2017-10-10 6:09 GMT+09:00 Douglas Greve >: You can't run i

Re: [Freesurfer] Qdec image considering multiple variables

So, I'm wondering if there is another way to draw statistical map considering multiple factors including missing variables. Thanks a lot. Kyung 2017-10-10 6:09 GMT+09:00 Douglas Greve : > You can't run it with missing variables > > On 10/9/17 12:40 AM, 박경일 wrote: > > Dear FS developer, > I am a

Re: [Freesurfer] Qdec image considering multiple variables

You can't run it with missing variables On 10/9/17 12:40 AM, 박경일 wrote: Dear FS developer, I am a FS beginner and trying to make QDEC images  of cortical thickness difference (color-coded inflated brain) between groups. No problem when fsid, diagnosis, age, and sex were only included in qdec.

Re: [Freesurfer] QDEC FDR for left and right hemispheres

On 09/12/2017 10:45 AM, Huang, Caleb (NIH/NINDS) [F] wrote: > > Hello, > > > When I run FDR on QDEC, I get different p-values for the left and > right hemispheres. Is it appropriate to use just one threshold for the > sake of consistency? > Probably so. There is not a way to do this from qdec.

Re: [Freesurfer] Qdec error in analysis

Can you send the command line, your key strokes and button presses, and the terminal output leading up to the error message? On 07/06/2017 12:27 AM, AYUSHI SHUKLA wrote: > Hi, > > Thank you for your response. > > Yes, I checked, and I do have the permission to read the file. > > Warm Regards > >

Re: [Freesurfer] Qdec error in analysis

Hi, Thank you for your response. Yes, I checked, and I do have the permission to read the file. Warm Regards Ayushi On Thu, 6 Jul 2017 at 09:42, Douglas Greve wrote: > Do you have read permission to that file? > > On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote: > > Hi, > > I'm a new user of qdec an

Re: [Freesurfer] Qdec error in analysis

Do you have read permission to that file? On 6/29/17 7:04 AM, AYUSHI SHUKLA wrote: Hi, I'm a new user of qdec and I'm trying to run a cortical thickness analysis in qdec between Schizophrenic patients and healthy controls. I have run "recon-all -i" and "recon-all -s -qcache" on my data and

Re: [Freesurfer] Qdec input fields

Sorry, qdec has been slowly losing functionality because no one here is maintaining it. Its a deprecated tool and we frequently do get reports of users being unable to manually input values into the boxes. Very odd indeed that your colleague can SSH into it and bypass the problem. Unfortunately

Re: [Freesurfer] qdec FindClustersAndGotoMax Plot ERROR

Sorry, qdec has been slowly losing functionality because no one here is maintaining it. This feature looks like one of the casualties. On 6/19/17 9:27 AM, Hossein Rejali wrote: Hello, I'm fairly new to freesurfer, I've been going through the tutorials to get my hands dirty. Currently on the

Re: [Freesurfer] Qdec 1.5

if that file does not exist, then it will crash. That file should be created by recon-all. Is that file not there? On 04/28/2017 05:22 AM, Duy Nguyen wrote: > Hello Douglas > > Thank you for your response. > I have just run the subjects from the data on OASIS through qdec and I > followed the s

Re: [Freesurfer] Qdec 1.5

Hello Douglas Thank you for your response. I have just run the subjects from the data on OASIS through qdec and I followed the steps on freesurfer. Everything is ok until the step of pressing 'Generate Stats Data Tables' that I have asked you before somehow I keep getting the same issue. There is

Re: [Freesurfer] QDEC and ROI drawing

sile.pins...@gmail.com> >> > <mailto:basile.pins...@gmail.com >> <mailto:basile.pins...@gmail.com>>>>>>>: >> > >> > >> > -- Forwarded message >> >

Re: [Freesurfer] QDEC and ROI drawing

lto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> > > >

Re: [Freesurfer] QDEC and ROI drawing

ailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> > > <mailto:gr...@n

Re: [Freesurfer] QDEC and ROI drawing

d.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harv

Re: [Freesurfer] QDEC and ROI drawing

<mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > &

Re: [Freesurfer] QDEC and ROI drawing

ile.pins...@gmail.com >> <mailto:basile.pins...@gmail.com>>>>: >> >> >> -- Forwarded message -- >> From: *Douglas N Greve* >> mailto:gr...@nmr.mgh.ha

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